Starting phenix.real_space_refine on Thu Jul 2 03:18:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p54_13194/07_2026/7p54_13194.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p54_13194/07_2026/7p54_13194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p54_13194/07_2026/7p54_13194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p54_13194/07_2026/7p54_13194.map" model { file = "/net/cci-nas-00/data/ceres_data/7p54_13194/07_2026/7p54_13194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p54_13194/07_2026/7p54_13194.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7p54_13194/07_2026/7p54_13194.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p54_13194/07_2026/7p54_13194.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 50 5.16 5 C 4030 2.51 5 N 986 2.21 5 O 1182 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6248 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3040 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 9, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3040 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 9, 'TRANS': 387} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.48, per 1000 atoms: 0.24 Number of scatterers: 6248 At special positions: 0 Unit cell: (93.744, 70.308, 128.898, 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 50 16.00 O 1182 8.00 N 986 7.00 C 4030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 382 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 382 " distance=2.02 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 367 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 601 " - " ASN A 283 " " NAG A 602 " - " ASN A 31 " " NAG B 601 " - " ASN B 283 " " NAG B 602 " - " ASN B 31 " " NAG C 1 " - " ASN A 352 " " NAG D 1 " - " ASN A 129 " " NAG E 1 " - " ASN B 352 " " NAG F 1 " - " ASN B 129 " Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 391.6 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1480 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 89.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 Processing helix chain 'A' and resid 38 through 72 Processing helix chain 'A' and resid 89 through 161 removed outlier: 4.269A pdb=" N LEU A 150 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 160 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 187 removed outlier: 3.744A pdb=" N LEU A 171 " --> pdb=" O TYR A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 237 Processing helix chain 'A' and resid 238 through 276 removed outlier: 3.560A pdb=" N SER A 244 " --> pdb=" O CYS A 240 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 308 through 337 removed outlier: 3.580A pdb=" N VAL A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 341 through 365 Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.482A pdb=" N LEU A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 409 Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.614A pdb=" N ALA A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 38 through 72 Processing helix chain 'B' and resid 89 through 161 removed outlier: 4.283A pdb=" N LEU B 150 " --> pdb=" O MET B 146 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 187 removed outlier: 3.773A pdb=" N LEU B 171 " --> pdb=" O TYR B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 237 Processing helix chain 'B' and resid 239 through 276 removed outlier: 4.272A pdb=" N ALA B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 285 Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 308 through 337 removed outlier: 3.597A pdb=" N VAL B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Proline residue: B 335 - end of helix Processing helix chain 'B' and resid 340 through 365 removed outlier: 3.772A pdb=" N LEU B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 383 removed outlier: 4.559A pdb=" N LEU B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 409 Processing helix chain 'B' and resid 409 through 416 removed outlier: 3.647A pdb=" N ALA B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) 581 hydrogen bonds defined for protein. 1743 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: 1.02 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1935 1.34 - 1.46: 1538 1.46 - 1.58: 2839 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 6378 Sorted by residual: bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.43e+00 bond pdb=" C1 NAG B 602 " pdb=" O5 NAG B 602 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.61e+00 ... (remaining 6373 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 8390 1.38 - 2.76: 254 2.76 - 4.13: 34 4.13 - 5.51: 11 5.51 - 6.89: 3 Bond angle restraints: 8692 Sorted by residual: angle pdb=" C VAL B 23 " pdb=" N GLY B 24 " pdb=" CA GLY B 24 " ideal model delta sigma weight residual 121.44 117.03 4.41 1.45e+00 4.76e-01 9.25e+00 angle pdb=" N GLN A 325 " pdb=" CA GLN A 325 " pdb=" CB GLN A 325 " ideal model delta sigma weight residual 110.16 114.31 -4.15 1.48e+00 4.57e-01 7.87e+00 angle pdb=" N ARG B 368 " pdb=" CA ARG B 368 " pdb=" C ARG B 368 " ideal model delta sigma weight residual 111.11 114.34 -3.23 1.20e+00 6.94e-01 7.25e+00 angle pdb=" N GLY B 37 " pdb=" CA GLY B 37 " pdb=" C GLY B 37 " ideal model delta sigma weight residual 114.25 111.02 3.23 1.30e+00 5.92e-01 6.18e+00 angle pdb=" C CYS B 367 " pdb=" N ARG B 368 " pdb=" CA ARG B 368 " ideal model delta sigma weight residual 120.54 123.89 -3.35 1.35e+00 5.49e-01 6.16e+00 ... (remaining 8687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 3250 16.06 - 32.12: 274 32.12 - 48.18: 75 48.18 - 64.23: 15 64.23 - 80.29: 8 Dihedral angle restraints: 3622 sinusoidal: 1318 harmonic: 2304 Sorted by residual: dihedral pdb=" CB CYS A 300 " pdb=" SG CYS A 300 " pdb=" SG CYS A 367 " pdb=" CB CYS A 367 " ideal model delta sinusoidal sigma weight residual -86.00 -162.49 76.49 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS B 300 " pdb=" SG CYS B 300 " pdb=" SG CYS B 367 " pdb=" CB CYS B 367 " ideal model delta sinusoidal sigma weight residual -86.00 -141.61 55.61 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS A 274 " pdb=" SG CYS A 274 " pdb=" SG CYS A 382 " pdb=" CB CYS A 382 " ideal model delta sinusoidal sigma weight residual 93.00 128.88 -35.88 1 1.00e+01 1.00e-02 1.82e+01 ... (remaining 3619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 985 0.063 - 0.126: 84 0.126 - 0.188: 1 0.188 - 0.251: 0 0.251 - 0.314: 2 Chirality restraints: 1072 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 129 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 129 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA GLN A 325 " pdb=" N GLN A 325 " pdb=" C GLN A 325 " pdb=" CB GLN A 325 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 1069 not shown) Planarity restraints: 1066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 20 " -0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO A 21 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 20 " -0.053 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO B 21 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 21 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 21 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 147 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C LYS B 147 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS B 147 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL B 148 " -0.009 2.00e-02 2.50e+03 ... (remaining 1063 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 737 2.74 - 3.28: 6440 3.28 - 3.82: 11254 3.82 - 4.36: 11217 4.36 - 4.90: 20634 Nonbonded interactions: 50282 Sorted by model distance: nonbonded pdb=" OD1 ASP A 278 " pdb=" OH TYR A 374 " model vdw 2.206 3.040 nonbonded pdb=" OD1 ASN B 111 " pdb=" NH1 ARG B 212 " model vdw 2.235 3.120 nonbonded pdb=" OD2 ASP A 38 " pdb=" OG SER A 40 " model vdw 2.237 3.040 nonbonded pdb=" O ILE B 281 " pdb=" OG1 THR B 285 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASN A 111 " pdb=" NH1 ARG A 212 " model vdw 2.243 3.120 ... (remaining 50277 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.750 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.560 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 0.038 6394 Z= 0.173 Angle : 0.586 7.623 8736 Z= 0.302 Chirality : 0.038 0.314 1072 Planarity : 0.005 0.083 1058 Dihedral : 13.629 80.293 2130 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.08 (0.29), residues: 786 helix: 3.32 (0.18), residues: 664 sheet: None (None), residues: 0 loop : -1.34 (0.49), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 192 TYR 0.010 0.001 TYR A 8 PHE 0.012 0.002 PHE B 395 TRP 0.007 0.001 TRP B 213 HIS 0.002 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 6378) covalent geometry : angle 0.55278 / 0.29 ( 8692) SS BOND : bond 0.00444 / 0.20 ( 4) SS BOND : angle 3.15677 / 1.77 ( 8) hydrogen bonds : bond 0.09394 / 6.09 ( 581) hydrogen bonds : angle 4.11908 / 3.14 ( 1743) link_BETA1-4 : bond 0.01212 / 0.55 ( 4) link_BETA1-4 : angle 4.04926 / 2.48 ( 12) link_NAG-ASN : bond 0.00337 / 0.20 ( 8) link_NAG-ASN : angle 1.63199 / 0.99 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.250 Fit side-chains REVERT: A 16 TRP cc_start: 0.6870 (m100) cc_final: 0.6646 (m100) REVERT: A 207 TYR cc_start: 0.7719 (t80) cc_final: 0.7392 (t80) REVERT: A 213 TRP cc_start: 0.8415 (t60) cc_final: 0.7703 (t-100) REVERT: A 245 MET cc_start: 0.6533 (mmp) cc_final: 0.6259 (mmp) REVERT: A 353 SER cc_start: 0.8925 (t) cc_final: 0.8714 (t) REVERT: B 12 TRP cc_start: 0.8176 (p-90) cc_final: 0.7966 (p-90) REVERT: B 213 TRP cc_start: 0.8324 (t60) cc_final: 0.7643 (t-100) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0792 time to fit residues: 14.1843 Evaluate side-chains 116 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.0470 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS B 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.150077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.119898 restraints weight = 7019.037| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.37 r_work: 0.3234 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6394 Z= 0.162 Angle : 0.538 6.525 8736 Z= 0.271 Chirality : 0.039 0.239 1072 Planarity : 0.004 0.054 1058 Dihedral : 3.690 19.790 844 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.67 % Allowed : 7.88 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.11 (0.29), residues: 786 helix: 3.41 (0.18), residues: 666 sheet: None (None), residues: 0 loop : -1.82 (0.50), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 295 TYR 0.020 0.002 TYR A 8 PHE 0.017 0.002 PHE A 62 TRP 0.017 0.001 TRP A 16 HIS 0.003 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 6378) covalent geometry : angle 0.51232 / 0.26 ( 8692) SS BOND : bond 0.00791 / 0.36 ( 4) SS BOND : angle 2.01429 / 1.13 ( 8) hydrogen bonds : bond 0.04091 / 2.71 ( 581) hydrogen bonds : angle 3.59863 / 2.73 ( 1743) link_BETA1-4 : bond 0.01115 / 0.51 ( 4) link_BETA1-4 : angle 3.29224 / 2.03 ( 12) link_NAG-ASN : bond 0.00282 / 0.19 ( 8) link_NAG-ASN : angle 1.90191 / 1.15 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.213 Fit side-chains REVERT: A 168 LEU cc_start: 0.8772 (mm) cc_final: 0.8569 (mm) REVERT: A 207 TYR cc_start: 0.8223 (t80) cc_final: 0.7793 (t80) REVERT: A 213 TRP cc_start: 0.8579 (t60) cc_final: 0.7724 (t-100) REVERT: A 245 MET cc_start: 0.6541 (mmp) cc_final: 0.5940 (mmp) REVERT: A 332 PHE cc_start: 0.7903 (m-10) cc_final: 0.7683 (m-10) REVERT: A 336 LEU cc_start: 0.8896 (mp) cc_final: 0.8685 (mp) REVERT: B 8 TYR cc_start: 0.7749 (t80) cc_final: 0.7460 (t80) REVERT: B 16 TRP cc_start: 0.8048 (m100) cc_final: 0.7821 (m100) REVERT: B 213 TRP cc_start: 0.8576 (t60) cc_final: 0.7647 (t-100) REVERT: B 283 ASN cc_start: 0.8226 (t0) cc_final: 0.7894 (t0) outliers start: 11 outliers final: 7 residues processed: 125 average time/residue: 0.0745 time to fit residues: 12.2384 Evaluate side-chains 123 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.156621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127486 restraints weight = 6965.620| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.28 r_work: 0.3202 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6394 Z= 0.161 Angle : 0.532 6.588 8736 Z= 0.263 Chirality : 0.038 0.233 1072 Planarity : 0.004 0.043 1058 Dihedral : 3.702 19.162 844 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.82 % Allowed : 12.58 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.09 (0.29), residues: 786 helix: 3.42 (0.18), residues: 668 sheet: None (None), residues: 0 loop : -2.10 (0.50), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 26 TYR 0.018 0.001 TYR A 8 PHE 0.023 0.002 PHE B 62 TRP 0.007 0.001 TRP A 16 HIS 0.003 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 6378) covalent geometry : angle 0.50845 / 0.26 ( 8692) SS BOND : bond 0.00873 / 0.39 ( 4) SS BOND : angle 1.63420 / 0.92 ( 8) hydrogen bonds : bond 0.03970 / 2.64 ( 581) hydrogen bonds : angle 3.55028 / 2.69 ( 1743) link_BETA1-4 : bond 0.01151 / 0.52 ( 4) link_BETA1-4 : angle 3.29682 / 2.03 ( 12) link_NAG-ASN : bond 0.00275 / 0.17 ( 8) link_NAG-ASN : angle 1.74109 / 1.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.154 Fit side-chains REVERT: A 168 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8595 (mm) REVERT: A 207 TYR cc_start: 0.8324 (t80) cc_final: 0.7871 (t80) REVERT: A 213 TRP cc_start: 0.8601 (t60) cc_final: 0.7694 (t-100) REVERT: A 251 LEU cc_start: 0.7619 (tt) cc_final: 0.7417 (tt) REVERT: A 283 ASN cc_start: 0.7988 (t0) cc_final: 0.7731 (t0) REVERT: A 332 PHE cc_start: 0.8061 (m-10) cc_final: 0.7672 (m-10) REVERT: A 336 LEU cc_start: 0.8916 (mp) cc_final: 0.8705 (mp) REVERT: B 8 TYR cc_start: 0.7607 (t80) cc_final: 0.7208 (t80) REVERT: B 16 TRP cc_start: 0.8004 (m100) cc_final: 0.7778 (m100) REVERT: B 213 TRP cc_start: 0.8597 (t60) cc_final: 0.7628 (t-100) REVERT: B 283 ASN cc_start: 0.8393 (t0) cc_final: 0.8047 (t0) outliers start: 12 outliers final: 9 residues processed: 129 average time/residue: 0.0734 time to fit residues: 12.5592 Evaluate side-chains 130 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122476 restraints weight = 7163.554| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.26 r_work: 0.3158 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 6394 Z= 0.248 Angle : 0.630 6.541 8736 Z= 0.312 Chirality : 0.043 0.230 1072 Planarity : 0.004 0.041 1058 Dihedral : 3.882 18.029 844 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.58 % Allowed : 15.91 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.54 (0.29), residues: 786 helix: 2.97 (0.18), residues: 678 sheet: None (None), residues: 0 loop : -2.25 (0.52), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 212 TYR 0.017 0.002 TYR A 8 PHE 0.027 0.002 PHE B 62 TRP 0.009 0.002 TRP A 414 HIS 0.004 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.25 ( 6378) covalent geometry : angle 0.60575 / 0.31 ( 8692) SS BOND : bond 0.01280 / 0.58 ( 4) SS BOND : angle 2.16923 / 1.20 ( 8) hydrogen bonds : bond 0.04321 / 2.89 ( 581) hydrogen bonds : angle 3.68359 / 2.79 ( 1743) link_BETA1-4 : bond 0.00992 / 0.45 ( 4) link_BETA1-4 : angle 3.38413 / 2.08 ( 12) link_NAG-ASN : bond 0.00375 / 0.23 ( 8) link_NAG-ASN : angle 2.02466 / 1.24 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.209 Fit side-chains REVERT: A 48 LEU cc_start: 0.8281 (mt) cc_final: 0.7996 (mt) REVERT: A 168 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8643 (mm) REVERT: A 207 TYR cc_start: 0.8531 (t80) cc_final: 0.7970 (t80) REVERT: A 213 TRP cc_start: 0.8562 (t60) cc_final: 0.7628 (t-100) REVERT: A 283 ASN cc_start: 0.8237 (t0) cc_final: 0.7954 (t0) REVERT: A 332 PHE cc_start: 0.8142 (m-10) cc_final: 0.7749 (m-10) REVERT: B 16 TRP cc_start: 0.7930 (m100) cc_final: 0.7635 (m100) REVERT: B 26 ARG cc_start: 0.7777 (mpp80) cc_final: 0.7475 (mpp80) REVERT: B 38 ASP cc_start: 0.7139 (t0) cc_final: 0.6847 (t0) REVERT: B 213 TRP cc_start: 0.8594 (t60) cc_final: 0.8333 (t-100) REVERT: B 283 ASN cc_start: 0.8470 (t0) cc_final: 0.8199 (t0) outliers start: 17 outliers final: 14 residues processed: 129 average time/residue: 0.0804 time to fit residues: 13.6583 Evaluate side-chains 129 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.154575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125040 restraints weight = 7064.052| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.32 r_work: 0.3172 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6394 Z= 0.150 Angle : 0.520 6.548 8736 Z= 0.263 Chirality : 0.038 0.240 1072 Planarity : 0.004 0.036 1058 Dihedral : 3.746 17.931 844 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.03 % Allowed : 17.27 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.91 (0.29), residues: 786 helix: 3.24 (0.18), residues: 678 sheet: None (None), residues: 0 loop : -2.29 (0.52), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.017 0.001 TYR A 8 PHE 0.026 0.002 PHE A 62 TRP 0.006 0.001 TRP A 16 HIS 0.003 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 6378) covalent geometry : angle 0.49707 / 0.26 ( 8692) SS BOND : bond 0.00917 / 0.42 ( 4) SS BOND : angle 1.67317 / 0.95 ( 8) hydrogen bonds : bond 0.03944 / 2.63 ( 581) hydrogen bonds : angle 3.52456 / 2.67 ( 1743) link_BETA1-4 : bond 0.01208 / 0.55 ( 4) link_BETA1-4 : angle 3.28815 / 2.02 ( 12) link_NAG-ASN : bond 0.00200 / 0.14 ( 8) link_NAG-ASN : angle 1.64829 / 0.98 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.217 Fit side-chains REVERT: A 26 ARG cc_start: 0.8186 (mtm110) cc_final: 0.7929 (mpp80) REVERT: A 168 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8605 (mm) REVERT: A 176 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7325 (tt0) REVERT: A 207 TYR cc_start: 0.8404 (t80) cc_final: 0.7925 (t80) REVERT: A 213 TRP cc_start: 0.8643 (t60) cc_final: 0.7550 (t-100) REVERT: A 283 ASN cc_start: 0.8170 (t0) cc_final: 0.7853 (t0) REVERT: A 325 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.6593 (mp10) REVERT: A 332 PHE cc_start: 0.8136 (m-10) cc_final: 0.7822 (m-10) REVERT: B 16 TRP cc_start: 0.7906 (m100) cc_final: 0.7539 (m100) REVERT: B 26 ARG cc_start: 0.7756 (mpp80) cc_final: 0.7431 (mpp80) REVERT: B 213 TRP cc_start: 0.8621 (t60) cc_final: 0.8300 (t-100) REVERT: B 283 ASN cc_start: 0.8464 (t0) cc_final: 0.8175 (t0) REVERT: B 332 PHE cc_start: 0.8109 (m-10) cc_final: 0.7848 (m-10) outliers start: 20 outliers final: 15 residues processed: 125 average time/residue: 0.0845 time to fit residues: 13.9608 Evaluate side-chains 127 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.0020 chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.155881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.126758 restraints weight = 6955.433| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.28 r_work: 0.3269 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6394 Z= 0.133 Angle : 0.506 7.795 8736 Z= 0.253 Chirality : 0.037 0.240 1072 Planarity : 0.004 0.033 1058 Dihedral : 3.690 18.489 844 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.88 % Allowed : 18.33 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.14 (0.29), residues: 786 helix: 3.38 (0.18), residues: 680 sheet: None (None), residues: 0 loop : -2.19 (0.53), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.016 0.001 TYR A 8 PHE 0.027 0.002 PHE A 62 TRP 0.007 0.001 TRP A 16 HIS 0.003 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 6378) covalent geometry : angle 0.48360 / 0.25 ( 8692) SS BOND : bond 0.00791 / 0.36 ( 4) SS BOND : angle 1.55979 / 0.89 ( 8) hydrogen bonds : bond 0.03804 / 2.53 ( 581) hydrogen bonds : angle 3.49600 / 2.64 ( 1743) link_BETA1-4 : bond 0.01234 / 0.57 ( 4) link_BETA1-4 : angle 3.22324 / 1.98 ( 12) link_NAG-ASN : bond 0.00216 / 0.14 ( 8) link_NAG-ASN : angle 1.54292 / 0.92 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.8112 (mtm110) cc_final: 0.7865 (mpp80) REVERT: A 176 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7390 (tt0) REVERT: A 207 TYR cc_start: 0.8471 (t80) cc_final: 0.7952 (t80) REVERT: A 213 TRP cc_start: 0.8608 (t60) cc_final: 0.7631 (t-100) REVERT: A 283 ASN cc_start: 0.8264 (t0) cc_final: 0.7946 (t0) REVERT: A 324 ILE cc_start: 0.9045 (mt) cc_final: 0.8773 (mt) REVERT: A 325 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.6544 (mp10) REVERT: B 8 TYR cc_start: 0.7785 (t80) cc_final: 0.7549 (t80) REVERT: B 16 TRP cc_start: 0.7959 (m100) cc_final: 0.7572 (m100) REVERT: B 26 ARG cc_start: 0.7801 (mpp80) cc_final: 0.7482 (mpp80) REVERT: B 213 TRP cc_start: 0.8648 (t60) cc_final: 0.7599 (t-100) REVERT: B 283 ASN cc_start: 0.8543 (t0) cc_final: 0.8257 (t0) REVERT: B 332 PHE cc_start: 0.8131 (m-10) cc_final: 0.7848 (m-10) outliers start: 19 outliers final: 17 residues processed: 128 average time/residue: 0.0845 time to fit residues: 14.2374 Evaluate side-chains 133 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 325 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 0.0020 chunk 12 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.155998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126990 restraints weight = 6949.535| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.26 r_work: 0.3227 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6394 Z= 0.132 Angle : 0.514 8.502 8736 Z= 0.255 Chirality : 0.037 0.235 1072 Planarity : 0.003 0.032 1058 Dihedral : 3.679 18.759 844 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.33 % Allowed : 18.94 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.25 (0.29), residues: 786 helix: 3.46 (0.18), residues: 680 sheet: None (None), residues: 0 loop : -2.21 (0.53), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.015 0.001 TYR A 8 PHE 0.029 0.002 PHE A 62 TRP 0.007 0.001 TRP A 16 HIS 0.003 0.001 HIS B 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 6378) covalent geometry : angle 0.49320 / 0.25 ( 8692) SS BOND : bond 0.00781 / 0.36 ( 4) SS BOND : angle 1.55295 / 0.88 ( 8) hydrogen bonds : bond 0.03730 / 2.49 ( 581) hydrogen bonds : angle 3.51843 / 2.64 ( 1743) link_BETA1-4 : bond 0.01208 / 0.55 ( 4) link_BETA1-4 : angle 3.22599 / 1.98 ( 12) link_NAG-ASN : bond 0.00214 / 0.14 ( 8) link_NAG-ASN : angle 1.48463 / 0.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.230 Fit side-chains REVERT: A 8 TYR cc_start: 0.7639 (t80) cc_final: 0.7375 (t80) REVERT: A 26 ARG cc_start: 0.8099 (mtm110) cc_final: 0.7844 (mpp80) REVERT: A 176 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7327 (tt0) REVERT: A 207 TYR cc_start: 0.8394 (t80) cc_final: 0.7875 (t80) REVERT: A 213 TRP cc_start: 0.8596 (t60) cc_final: 0.7539 (t-100) REVERT: A 283 ASN cc_start: 0.8218 (t0) cc_final: 0.7881 (t0) REVERT: A 324 ILE cc_start: 0.9016 (mt) cc_final: 0.8739 (mt) REVERT: A 325 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.6504 (mp10) REVERT: B 16 TRP cc_start: 0.7951 (m100) cc_final: 0.7575 (m100) REVERT: B 26 ARG cc_start: 0.7778 (mpp80) cc_final: 0.7476 (mpp80) REVERT: B 213 TRP cc_start: 0.8634 (t60) cc_final: 0.7576 (t-100) REVERT: B 283 ASN cc_start: 0.8517 (t0) cc_final: 0.8228 (t0) REVERT: B 325 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7047 (mp10) REVERT: B 332 PHE cc_start: 0.8177 (m-10) cc_final: 0.7867 (m-10) outliers start: 22 outliers final: 17 residues processed: 133 average time/residue: 0.0819 time to fit residues: 14.3968 Evaluate side-chains 135 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 0.0770 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 70 optimal weight: 0.0770 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.157342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.128006 restraints weight = 6981.245| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.30 r_work: 0.3267 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6394 Z= 0.119 Angle : 0.501 7.891 8736 Z= 0.250 Chirality : 0.037 0.234 1072 Planarity : 0.003 0.032 1058 Dihedral : 3.644 18.555 844 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.73 % Allowed : 19.85 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.38 (0.29), residues: 786 helix: 3.55 (0.18), residues: 680 sheet: None (None), residues: 0 loop : -2.22 (0.53), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.017 0.001 TYR B 8 PHE 0.029 0.002 PHE A 62 TRP 0.008 0.001 TRP A 16 HIS 0.002 0.001 HIS B 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 6378) covalent geometry : angle 0.48100 / 0.25 ( 8692) SS BOND : bond 0.00617 / 0.29 ( 4) SS BOND : angle 1.42963 / 0.82 ( 8) hydrogen bonds : bond 0.03611 / 2.40 ( 581) hydrogen bonds : angle 3.48708 / 2.61 ( 1743) link_BETA1-4 : bond 0.01247 / 0.57 ( 4) link_BETA1-4 : angle 3.18955 / 1.96 ( 12) link_NAG-ASN : bond 0.00228 / 0.14 ( 8) link_NAG-ASN : angle 1.37872 / 0.83 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.212 Fit side-chains REVERT: A 26 ARG cc_start: 0.8101 (mtm110) cc_final: 0.7843 (mpp80) REVERT: A 207 TYR cc_start: 0.8344 (t80) cc_final: 0.7859 (t80) REVERT: A 213 TRP cc_start: 0.8570 (t60) cc_final: 0.7569 (t-100) REVERT: A 283 ASN cc_start: 0.8252 (t0) cc_final: 0.7923 (t0) REVERT: A 324 ILE cc_start: 0.9036 (mt) cc_final: 0.8734 (mt) REVERT: A 325 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.6520 (mp10) REVERT: A 332 PHE cc_start: 0.8418 (m-80) cc_final: 0.8184 (m-10) REVERT: B 8 TYR cc_start: 0.7311 (t80) cc_final: 0.7043 (t80) REVERT: B 16 TRP cc_start: 0.7949 (m100) cc_final: 0.7568 (m100) REVERT: B 26 ARG cc_start: 0.7789 (mpp80) cc_final: 0.7489 (mpp80) REVERT: B 213 TRP cc_start: 0.8605 (t60) cc_final: 0.7544 (t-100) REVERT: B 283 ASN cc_start: 0.8533 (t0) cc_final: 0.8235 (t0) REVERT: B 325 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.6889 (mp10) REVERT: B 332 PHE cc_start: 0.8181 (m-10) cc_final: 0.7798 (m-10) REVERT: B 336 LEU cc_start: 0.8656 (mt) cc_final: 0.8346 (mp) outliers start: 18 outliers final: 16 residues processed: 137 average time/residue: 0.0820 time to fit residues: 14.7965 Evaluate side-chains 140 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 0.0050 chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.157248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.127871 restraints weight = 6958.742| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.30 r_work: 0.3266 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6394 Z= 0.124 Angle : 0.510 7.726 8736 Z= 0.252 Chirality : 0.037 0.230 1072 Planarity : 0.003 0.030 1058 Dihedral : 3.630 18.873 844 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.73 % Allowed : 20.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.42 (0.29), residues: 786 helix: 3.58 (0.18), residues: 680 sheet: None (None), residues: 0 loop : -2.20 (0.53), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.016 0.001 TYR B 8 PHE 0.028 0.002 PHE A 62 TRP 0.009 0.001 TRP A 16 HIS 0.002 0.001 HIS B 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 6378) covalent geometry : angle 0.49033 / 0.25 ( 8692) SS BOND : bond 0.00689 / 0.32 ( 4) SS BOND : angle 1.42971 / 0.82 ( 8) hydrogen bonds : bond 0.03591 / 2.40 ( 581) hydrogen bonds : angle 3.48294 / 2.61 ( 1743) link_BETA1-4 : bond 0.01238 / 0.56 ( 4) link_BETA1-4 : angle 3.20848 / 1.97 ( 12) link_NAG-ASN : bond 0.00225 / 0.14 ( 8) link_NAG-ASN : angle 1.37091 / 0.82 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.219 Fit side-chains REVERT: A 8 TYR cc_start: 0.7188 (t80) cc_final: 0.6843 (t80) REVERT: A 26 ARG cc_start: 0.8072 (mtm110) cc_final: 0.7809 (mpp80) REVERT: A 207 TYR cc_start: 0.8330 (t80) cc_final: 0.7873 (t80) REVERT: A 213 TRP cc_start: 0.8570 (t60) cc_final: 0.7578 (t-100) REVERT: A 283 ASN cc_start: 0.8268 (t0) cc_final: 0.7925 (t0) REVERT: A 325 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.6611 (mp10) REVERT: B 16 TRP cc_start: 0.7953 (m100) cc_final: 0.7565 (m100) REVERT: B 26 ARG cc_start: 0.7783 (mpp80) cc_final: 0.7481 (mpp80) REVERT: B 213 TRP cc_start: 0.8596 (t60) cc_final: 0.7556 (t-100) REVERT: B 283 ASN cc_start: 0.8532 (t0) cc_final: 0.8237 (t0) REVERT: B 325 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.6881 (mp10) REVERT: B 332 PHE cc_start: 0.8218 (m-10) cc_final: 0.7850 (m-10) REVERT: B 336 LEU cc_start: 0.8633 (mt) cc_final: 0.8321 (mp) outliers start: 18 outliers final: 15 residues processed: 131 average time/residue: 0.0851 time to fit residues: 14.6339 Evaluate side-chains 135 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.155962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126768 restraints weight = 6999.609| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.29 r_work: 0.3190 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6394 Z= 0.143 Angle : 0.530 7.423 8736 Z= 0.263 Chirality : 0.038 0.231 1072 Planarity : 0.004 0.038 1058 Dihedral : 3.660 18.623 844 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.73 % Allowed : 21.36 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.34 (0.29), residues: 786 helix: 3.52 (0.18), residues: 680 sheet: None (None), residues: 0 loop : -2.21 (0.53), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.019 0.001 TYR A 216 PHE 0.030 0.002 PHE A 62 TRP 0.009 0.001 TRP A 16 HIS 0.003 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 6378) covalent geometry : angle 0.50959 / 0.26 ( 8692) SS BOND : bond 0.00786 / 0.36 ( 4) SS BOND : angle 1.58578 / 0.91 ( 8) hydrogen bonds : bond 0.03673 / 2.45 ( 581) hydrogen bonds : angle 3.53375 / 2.65 ( 1743) link_BETA1-4 : bond 0.01189 / 0.54 ( 4) link_BETA1-4 : angle 3.21797 / 1.97 ( 12) link_NAG-ASN : bond 0.00217 / 0.14 ( 8) link_NAG-ASN : angle 1.44381 / 0.87 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 8 TYR cc_start: 0.7133 (t80) cc_final: 0.6787 (t80) REVERT: A 26 ARG cc_start: 0.8074 (mtm110) cc_final: 0.7819 (mpp80) REVERT: A 207 TYR cc_start: 0.8290 (t80) cc_final: 0.7785 (t80) REVERT: A 213 TRP cc_start: 0.8593 (t60) cc_final: 0.7503 (t-100) REVERT: A 283 ASN cc_start: 0.8185 (t0) cc_final: 0.7837 (t0) REVERT: A 325 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.6504 (mp10) REVERT: B 8 TYR cc_start: 0.7296 (t80) cc_final: 0.6859 (t80) REVERT: B 16 TRP cc_start: 0.7962 (m100) cc_final: 0.7529 (m100) REVERT: B 26 ARG cc_start: 0.7772 (mpp80) cc_final: 0.7512 (mpp80) REVERT: B 213 TRP cc_start: 0.8617 (t60) cc_final: 0.7482 (t-100) REVERT: B 283 ASN cc_start: 0.8455 (t0) cc_final: 0.8156 (t0) REVERT: B 332 PHE cc_start: 0.8232 (m-10) cc_final: 0.7866 (m-10) REVERT: B 336 LEU cc_start: 0.8650 (mt) cc_final: 0.8318 (mp) outliers start: 18 outliers final: 17 residues processed: 131 average time/residue: 0.0858 time to fit residues: 14.7746 Evaluate side-chains 135 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.156207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126858 restraints weight = 7014.823| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.31 r_work: 0.3252 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6394 Z= 0.140 Angle : 0.528 7.658 8736 Z= 0.262 Chirality : 0.038 0.232 1072 Planarity : 0.003 0.036 1058 Dihedral : 3.665 18.948 844 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.73 % Allowed : 21.36 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.34 (0.29), residues: 786 helix: 3.52 (0.18), residues: 680 sheet: None (None), residues: 0 loop : -2.20 (0.53), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.017 0.001 TYR A 216 PHE 0.030 0.002 PHE A 62 TRP 0.010 0.001 TRP A 16 HIS 0.003 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 6378) covalent geometry : angle 0.50841 / 0.26 ( 8692) SS BOND : bond 0.00753 / 0.34 ( 4) SS BOND : angle 1.59347 / 0.92 ( 8) hydrogen bonds : bond 0.03681 / 2.46 ( 581) hydrogen bonds : angle 3.53118 / 2.65 ( 1743) link_BETA1-4 : bond 0.01209 / 0.55 ( 4) link_BETA1-4 : angle 3.21045 / 1.97 ( 12) link_NAG-ASN : bond 0.00209 / 0.14 ( 8) link_NAG-ASN : angle 1.42350 / 0.85 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1557.49 seconds wall clock time: 27 minutes 32.14 seconds (1652.14 seconds total)