Starting phenix.real_space_refine on Wed Jul 1 20:46:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7usb_26731/07_2026/7usb_26731.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usb_26731/07_2026/7usb_26731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7usb_26731/07_2026/7usb_26731.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7usb_26731/07_2026/7usb_26731.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7usb_26731/07_2026/7usb_26731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usb_26731/07_2026/7usb_26731.map" model { file = "/net/cci-nas-00/data/ceres_data/7usb_26731/07_2026/7usb_26731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usb_26731/07_2026/7usb_26731.cif" } resolution = 3.1 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= 0.026 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 12 5.16 5 C 1078 2.51 5 N 279 2.21 5 O 292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 1661 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain breaks: 5 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 5, 'GLU:plan': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 84 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 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.72, per 1000 atoms: 0.43 Number of scatterers: 1661 At special positions: 0 Unit cell: (57.324, 67.44, 57.324, 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 12 16.00 O 292 8.00 N 279 7.00 C 1078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 68 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 170 " distance=2.04 Simple disulfide: pdb=" SG CYS A 250 " - pdb=" SG CYS A 254 " distance=2.13 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 B 1 " - " NAG B 2 " NAG-ASN " NAG A5401 " - " ASN A 242 " " NAG A5402 " - " ASN A 26 " " NAG A5403 " - " ASN A 42 " " NAG B 1 " - " ASN A 249 " Time building additional restraints: 0.16 Conformation dependent library (CDL) restraints added in 72.8 milliseconds 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 404 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 4 sheets defined 13.6% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 29 through 32 Processing helix chain 'A' and resid 33 through 44 Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 254 through 258 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 57 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 80 removed outlier: 7.297A pdb=" N PHE A 202 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LYS A 110 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR A 204 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 130 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU A 155 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE A 132 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS A 153 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 196 64 hydrogen bonds defined for protein. 150 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: 0.23 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 390 1.33 - 1.46: 470 1.46 - 1.58: 830 1.58 - 1.71: 1 1.71 - 1.84: 14 Bond restraints: 1705 Sorted by residual: bond pdb=" CB LEU A 207 " pdb=" CG LEU A 207 " ideal model delta sigma weight residual 1.530 1.602 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" CA PRO A 48 " pdb=" C PRO A 48 " ideal model delta sigma weight residual 1.514 1.534 -0.019 5.50e-03 3.31e+04 1.23e+01 bond pdb=" C5 NAG A5401 " pdb=" O5 NAG A5401 " ideal model delta sigma weight residual 1.413 1.478 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C5 NAG A5402 " pdb=" O5 NAG A5402 " ideal model delta sigma weight residual 1.413 1.475 -0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" NE ARG A 194 " pdb=" CZ ARG A 194 " ideal model delta sigma weight residual 1.326 1.358 -0.032 1.10e-02 8.26e+03 8.45e+00 ... (remaining 1700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.50: 2285 4.50 - 8.99: 46 8.99 - 13.49: 2 13.49 - 17.98: 2 17.98 - 22.48: 2 Bond angle restraints: 2337 Sorted by residual: angle pdb=" CD1 LEU A 41 " pdb=" CG LEU A 41 " pdb=" CD2 LEU A 41 " ideal model delta sigma weight residual 110.80 133.28 -22.48 2.20e+00 2.07e-01 1.04e+02 angle pdb=" C LEU A 47 " pdb=" N PRO A 48 " pdb=" CA PRO A 48 " ideal model delta sigma weight residual 119.66 127.07 -7.41 7.30e-01 1.88e+00 1.03e+02 angle pdb=" CG1 VAL A 185 " pdb=" CB VAL A 185 " pdb=" CG2 VAL A 185 " ideal model delta sigma weight residual 110.80 131.09 -20.29 2.20e+00 2.07e-01 8.50e+01 angle pdb=" C PRO A 48 " pdb=" N PRO A 49 " pdb=" CA PRO A 49 " ideal model delta sigma weight residual 119.56 127.28 -7.72 1.01e+00 9.80e-01 5.84e+01 angle pdb=" C PRO A 137 " pdb=" N PRO A 138 " pdb=" CA PRO A 138 " ideal model delta sigma weight residual 120.03 126.02 -5.99 9.90e-01 1.02e+00 3.67e+01 ... (remaining 2332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 893 17.81 - 35.63: 33 35.63 - 53.44: 7 53.44 - 71.25: 6 71.25 - 89.07: 1 Dihedral angle restraints: 940 sinusoidal: 317 harmonic: 623 Sorted by residual: dihedral pdb=" CB CYS A 21 " pdb=" SG CYS A 21 " pdb=" SG CYS A 68 " pdb=" CB CYS A 68 " ideal model delta sinusoidal sigma weight residual 93.00 162.97 -69.97 1 1.00e+01 1.00e-02 6.31e+01 dihedral pdb=" CB CYS A 250 " pdb=" SG CYS A 250 " pdb=" SG CYS A 254 " pdb=" CB CYS A 254 " ideal model delta sinusoidal sigma weight residual 93.00 153.68 -60.68 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 147 " pdb=" CB CYS A 147 " ideal model delta sinusoidal sigma weight residual -86.00 -142.30 56.30 1 1.00e+01 1.00e-02 4.27e+01 ... (remaining 937 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.109: 226 0.109 - 0.216: 31 0.216 - 0.323: 11 0.323 - 0.430: 6 0.430 - 0.537: 2 Chirality restraints: 276 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.73e+01 chirality pdb=" CG LEU A 41 " pdb=" CB LEU A 41 " pdb=" CD1 LEU A 41 " pdb=" CD2 LEU A 41 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.21e+00 chirality pdb=" CB VAL A 185 " pdb=" CA VAL A 185 " pdb=" CG1 VAL A 185 " pdb=" CG2 VAL A 185 " both_signs ideal model delta sigma weight residual False -2.63 -2.10 -0.52 2.00e-01 2.50e+01 6.87e+00 ... (remaining 273 not shown) Planarity restraints: 293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A5403 " -0.211 2.00e-02 2.50e+03 1.79e-01 4.01e+02 pdb=" C7 NAG A5403 " 0.043 2.00e-02 2.50e+03 pdb=" C8 NAG A5403 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG A5403 " 0.294 2.00e-02 2.50e+03 pdb=" O7 NAG A5403 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.103 2.00e-02 2.50e+03 8.70e-02 9.46e+01 pdb=" C7 NAG B 2 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.028 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.138 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 133 " -0.021 2.00e-02 2.50e+03 4.13e-02 1.70e+01 pdb=" C CYS A 133 " 0.071 2.00e-02 2.50e+03 pdb=" O CYS A 133 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS A 134 " -0.024 2.00e-02 2.50e+03 ... (remaining 290 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 931 3.05 - 3.51: 1400 3.51 - 3.98: 2544 3.98 - 4.44: 2901 4.44 - 4.90: 4618 Nonbonded interactions: 12394 Sorted by model distance: nonbonded pdb=" N GLY A 243 " pdb=" N THR A 244 " model vdw 2.590 2.560 nonbonded pdb=" N PHE A 202 " pdb=" O PHE A 202 " model vdw 2.614 2.496 nonbonded pdb=" O LYS A 110 " pdb=" CD PRO A 111 " model vdw 2.626 2.752 nonbonded pdb=" OD1 ASP A 89 " pdb=" N TYR A 90 " model vdw 2.634 3.120 nonbonded pdb=" N GLN A 167 " pdb=" O GLN A 167 " model vdw 2.647 2.496 ... (remaining 12389 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.030 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.000 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.013 0.100 1715 Z= 0.730 Angle : 1.738 22.477 2362 Z= 1.051 Chirality : 0.110 0.537 276 Planarity : 0.013 0.179 289 Dihedral : 10.686 89.066 521 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.39 % Allowed : 1.39 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.53), residues: 201 helix: -1.80 (0.97), residues: 18 sheet: 1.28 (0.53), residues: 75 loop : -1.01 (0.52), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 46 TYR 0.023 0.005 TYR A 90 PHE 0.009 0.003 PHE A 227 TRP 0.022 0.005 TRP A 88 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.01297 / 0.71 ( 1705) covalent geometry : angle 1.72012 / 1.05 ( 2337) SS BOND : bond 0.04489 / 3.37 ( 5) SS BOND : angle 2.96757 / 1.75 ( 10) hydrogen bonds : bond 0.17079 / 10.23 ( 64) hydrogen bonds : angle 6.90121 / 5.17 ( 150) link_BETA1-4 : bond 0.00680 / 0.36 ( 1) link_BETA1-4 : angle 4.32483 / 2.26 ( 3) link_NAG-ASN : bond 0.05775 / 2.93 ( 4) link_NAG-ASN : angle 2.53008 / 1.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.065 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.0444 time to fit residues: 1.8878 Evaluate side-chains 18 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.0970 chunk 8 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.0980 chunk 4 optimal weight: 0.0670 overall best weight: 0.1316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN A 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.181109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.153048 restraints weight = 2038.425| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.44 r_work: 0.3634 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1715 Z= 0.144 Angle : 0.677 6.020 2362 Z= 0.358 Chirality : 0.049 0.234 276 Planarity : 0.004 0.032 289 Dihedral : 5.170 15.600 226 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.69 % Allowed : 6.25 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.54), residues: 201 helix: 1.72 (1.41), residues: 12 sheet: 1.02 (0.56), residues: 75 loop : -1.15 (0.50), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 154 TYR 0.008 0.001 TYR A 175 PHE 0.012 0.001 PHE A 24 TRP 0.010 0.001 TRP A 88 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 1705) covalent geometry : angle 0.63510 / 0.35 ( 2337) SS BOND : bond 0.00828 / 0.42 ( 5) SS BOND : angle 0.58315 / 0.34 ( 10) hydrogen bonds : bond 0.05287 / 3.15 ( 64) hydrogen bonds : angle 5.35032 / 4.10 ( 150) link_BETA1-4 : bond 0.00351 / 0.18 ( 1) link_BETA1-4 : angle 2.54432 / 1.35 ( 3) link_NAG-ASN : bond 0.00393 / 0.20 ( 4) link_NAG-ASN : angle 3.14216 / 1.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.063 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.0698 time to fit residues: 1.6177 Evaluate side-chains 18 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 4 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.0970 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 2 optimal weight: 0.0010 overall best weight: 0.1384 ------------------------------------------------------------------------------- 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 = 0.4267 r_free = 0.4267 target = 0.196097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.167059 restraints weight = 1956.996| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.43 r_work: 0.3807 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1715 Z= 0.116 Angle : 0.576 5.611 2362 Z= 0.301 Chirality : 0.047 0.216 276 Planarity : 0.004 0.032 289 Dihedral : 4.863 15.357 225 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.39 % Allowed : 7.64 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.54), residues: 201 helix: 1.29 (1.34), residues: 13 sheet: 0.82 (0.55), residues: 74 loop : -1.44 (0.51), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 154 TYR 0.007 0.001 TYR A 175 PHE 0.007 0.001 PHE A 180 TRP 0.009 0.001 TRP A 88 HIS 0.001 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 1705) covalent geometry : angle 0.54092 / 0.29 ( 2337) SS BOND : bond 0.00166 / 0.09 ( 5) SS BOND : angle 0.48846 / 0.28 ( 10) hydrogen bonds : bond 0.03934 / 2.37 ( 64) hydrogen bonds : angle 4.95984 / 3.81 ( 150) link_BETA1-4 : bond 0.00137 / 0.07 ( 1) link_BETA1-4 : angle 1.79821 / 0.97 ( 3) link_NAG-ASN : bond 0.00321 / 0.16 ( 4) link_NAG-ASN : angle 2.71782 / 1.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.065 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 18 average time/residue: 0.0534 time to fit residues: 1.1880 Evaluate side-chains 18 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.0000 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.3384 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.171781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141020 restraints weight = 1981.069| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.51 r_work: 0.3528 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 1715 Z= 0.201 Angle : 0.668 6.618 2362 Z= 0.336 Chirality : 0.051 0.249 276 Planarity : 0.004 0.031 289 Dihedral : 5.229 16.714 225 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.08 % Allowed : 7.64 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.56), residues: 201 helix: 0.77 (1.28), residues: 13 sheet: 0.43 (0.60), residues: 73 loop : -1.54 (0.54), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 46 TYR 0.009 0.001 TYR A 112 PHE 0.010 0.002 PHE A 59 TRP 0.006 0.001 TRP A 88 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 ( 1705) covalent geometry : angle 0.61841 / 0.33 ( 2337) SS BOND : bond 0.00347 / 0.21 ( 5) SS BOND : angle 0.66881 / 0.37 ( 10) hydrogen bonds : bond 0.04173 / 2.59 ( 64) hydrogen bonds : angle 5.04592 / 3.88 ( 150) link_BETA1-4 : bond 0.00135 / 0.07 ( 1) link_BETA1-4 : angle 2.35754 / 1.23 ( 3) link_NAG-ASN : bond 0.00369 / 0.19 ( 4) link_NAG-ASN : angle 3.39299 / 1.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.066 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 21 average time/residue: 0.0610 time to fit residues: 1.5335 Evaluate side-chains 21 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 1 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.0970 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.170332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139486 restraints weight = 2008.692| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.52 r_work: 0.3511 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 1715 Z= 0.193 Angle : 0.652 6.676 2362 Z= 0.328 Chirality : 0.050 0.249 276 Planarity : 0.004 0.032 289 Dihedral : 5.151 16.053 225 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.78 % Allowed : 9.72 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.57), residues: 201 helix: 0.81 (1.32), residues: 13 sheet: 0.24 (0.61), residues: 73 loop : -1.61 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 46 TYR 0.006 0.001 TYR A 112 PHE 0.020 0.002 PHE A 159 TRP 0.009 0.001 TRP A 88 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 ( 1705) covalent geometry : angle 0.60171 / 0.32 ( 2337) SS BOND : bond 0.00261 / 0.15 ( 5) SS BOND : angle 0.52481 / 0.29 ( 10) hydrogen bonds : bond 0.03986 / 2.50 ( 64) hydrogen bonds : angle 5.02493 / 3.85 ( 150) link_BETA1-4 : bond 0.00284 / 0.15 ( 1) link_BETA1-4 : angle 2.26130 / 1.20 ( 3) link_NAG-ASN : bond 0.00436 / 0.22 ( 4) link_NAG-ASN : angle 3.40137 / 1.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.059 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 23 average time/residue: 0.0568 time to fit residues: 1.5501 Evaluate side-chains 25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 0.0570 chunk 1 optimal weight: 0.0980 chunk 15 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 5 optimal weight: 0.3980 chunk 14 optimal weight: 0.0980 chunk 2 optimal weight: 0.0970 chunk 12 optimal weight: 0.2980 chunk 13 optimal weight: 0.4980 overall best weight: 0.1296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.173403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.142995 restraints weight = 1965.821| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.50 r_work: 0.3727 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 1715 Z= 0.104 Angle : 0.538 5.490 2362 Z= 0.277 Chirality : 0.046 0.221 276 Planarity : 0.003 0.030 289 Dihedral : 4.646 14.616 225 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.08 % Allowed : 9.72 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.58), residues: 201 helix: 1.03 (1.32), residues: 13 sheet: 0.13 (0.60), residues: 74 loop : -1.46 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 194 TYR 0.005 0.001 TYR A 43 PHE 0.022 0.002 PHE A 159 TRP 0.008 0.001 TRP A 88 HIS 0.001 0.000 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 ( 1705) covalent geometry : angle 0.50175 / 0.27 ( 2337) SS BOND : bond 0.00306 / 0.15 ( 5) SS BOND : angle 0.49550 / 0.31 ( 10) hydrogen bonds : bond 0.03404 / 2.12 ( 64) hydrogen bonds : angle 4.75424 / 3.64 ( 150) link_BETA1-4 : bond 0.00098 / 0.05 ( 1) link_BETA1-4 : angle 1.76305 / 0.98 ( 3) link_NAG-ASN : bond 0.00349 / 0.17 ( 4) link_NAG-ASN : angle 2.62109 / 1.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.060 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.0500 time to fit residues: 1.5600 Evaluate side-chains 26 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 2 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.169509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.139092 restraints weight = 1967.575| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.49 r_work: 0.3501 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 1715 Z= 0.212 Angle : 0.649 6.245 2362 Z= 0.323 Chirality : 0.050 0.246 276 Planarity : 0.004 0.030 289 Dihedral : 5.016 15.765 225 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.08 % Allowed : 10.42 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.58), residues: 201 helix: 0.85 (1.32), residues: 13 sheet: 0.02 (0.62), residues: 73 loop : -1.65 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 237 TYR 0.006 0.001 TYR A 58 PHE 0.018 0.002 PHE A 159 TRP 0.007 0.001 TRP A 88 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.21 ( 1705) covalent geometry : angle 0.60050 / 0.31 ( 2337) SS BOND : bond 0.00321 / 0.20 ( 5) SS BOND : angle 0.56563 / 0.30 ( 10) hydrogen bonds : bond 0.03914 / 2.47 ( 64) hydrogen bonds : angle 5.01275 / 3.83 ( 150) link_BETA1-4 : bond 0.00320 / 0.17 ( 1) link_BETA1-4 : angle 2.32547 / 1.22 ( 3) link_NAG-ASN : bond 0.00420 / 0.22 ( 4) link_NAG-ASN : angle 3.32007 / 1.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.041 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 28 average time/residue: 0.0502 time to fit residues: 1.6079 Evaluate side-chains 28 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.0570 chunk 18 optimal weight: 0.1980 chunk 8 optimal weight: 0.0870 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 chunk 1 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.0870 overall best weight: 0.0830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.174094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.144094 restraints weight = 1959.777| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.51 r_work: 0.3554 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 1715 Z= 0.128 Angle : 0.730 13.416 2362 Z= 0.368 Chirality : 0.046 0.221 276 Planarity : 0.003 0.028 289 Dihedral : 5.097 25.924 225 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.78 % Allowed : 10.42 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.57), residues: 201 helix: 0.94 (1.33), residues: 13 sheet: 0.02 (0.61), residues: 74 loop : -1.74 (0.54), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 237 TYR 0.009 0.001 TYR A 77 PHE 0.024 0.001 PHE A 159 TRP 0.008 0.001 TRP A 88 HIS 0.001 0.000 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 1705) covalent geometry : angle 0.65849 / 0.34 ( 2337) SS BOND : bond 0.00163 / 0.11 ( 5) SS BOND : angle 3.73540 / 2.41 ( 10) hydrogen bonds : bond 0.03444 / 2.23 ( 64) hydrogen bonds : angle 4.83482 / 3.69 ( 150) link_BETA1-4 : bond 0.00110 / 0.06 ( 1) link_BETA1-4 : angle 1.79250 / 1.01 ( 3) link_NAG-ASN : bond 0.00779 / 0.39 ( 4) link_NAG-ASN : angle 2.84028 / 1.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.063 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 0.0556 time to fit residues: 1.7464 Evaluate side-chains 26 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.0980 chunk 4 optimal weight: 0.0060 chunk 9 optimal weight: 0.3980 chunk 6 optimal weight: 0.4980 chunk 0 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.0870 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 overall best weight: 0.1574 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.172221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141996 restraints weight = 2002.144| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.56 r_work: 0.3507 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 1715 Z= 0.137 Angle : 0.688 11.187 2362 Z= 0.346 Chirality : 0.047 0.221 276 Planarity : 0.003 0.026 289 Dihedral : 5.125 28.142 225 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.08 % Allowed : 11.81 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.57), residues: 201 helix: 0.99 (1.34), residues: 13 sheet: -0.03 (0.61), residues: 74 loop : -1.69 (0.55), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 46 TYR 0.007 0.001 TYR A 257 PHE 0.019 0.001 PHE A 159 TRP 0.007 0.001 TRP A 88 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 1705) covalent geometry : angle 0.62438 / 0.33 ( 2337) SS BOND : bond 0.00219 / 0.12 ( 5) SS BOND : angle 3.19122 / 2.05 ( 10) hydrogen bonds : bond 0.03709 / 2.44 ( 64) hydrogen bonds : angle 4.80660 / 3.69 ( 150) link_BETA1-4 : bond 0.00055 / 0.03 ( 1) link_BETA1-4 : angle 1.56975 / 0.82 ( 3) link_NAG-ASN : bond 0.00535 / 0.27 ( 4) link_NAG-ASN : angle 2.86098 / 1.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.036 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.0404 time to fit residues: 1.2232 Evaluate side-chains 26 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 0.4980 chunk 18 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 13 optimal weight: 0.0030 overall best weight: 0.1990 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.172186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.142160 restraints weight = 1971.868| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.54 r_work: 0.3585 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 1715 Z= 0.149 Angle : 0.661 8.729 2362 Z= 0.335 Chirality : 0.047 0.226 276 Planarity : 0.003 0.028 289 Dihedral : 5.041 24.934 225 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.08 % Allowed : 13.19 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.56), residues: 201 helix: -0.67 (1.07), residues: 19 sheet: 0.15 (0.61), residues: 72 loop : -1.64 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 46 TYR 0.008 0.001 TYR A 77 PHE 0.022 0.001 PHE A 159 TRP 0.007 0.001 TRP A 88 HIS 0.001 0.000 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 1705) covalent geometry : angle 0.59748 / 0.32 ( 2337) SS BOND : bond 0.00161 / 0.09 ( 5) SS BOND : angle 2.76604 / 1.76 ( 10) hydrogen bonds : bond 0.03743 / 2.48 ( 64) hydrogen bonds : angle 4.84797 / 3.70 ( 150) link_BETA1-4 : bond 0.00165 / 0.09 ( 1) link_BETA1-4 : angle 1.69158 / 0.91 ( 3) link_NAG-ASN : bond 0.00566 / 0.28 ( 4) link_NAG-ASN : angle 3.08200 / 1.80 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.035 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.0419 time to fit residues: 1.1610 Evaluate side-chains 26 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.1980 chunk 6 optimal weight: 0.4980 chunk 5 optimal weight: 0.0870 chunk 16 optimal weight: 0.0870 chunk 19 optimal weight: 0.5980 overall best weight: 0.2936 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.169806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139182 restraints weight = 1975.898| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.57 r_work: 0.3459 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 1715 Z= 0.193 Angle : 0.720 9.651 2362 Z= 0.361 Chirality : 0.049 0.236 276 Planarity : 0.004 0.029 289 Dihedral : 5.112 19.276 225 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.08 % Allowed : 13.19 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.56), residues: 201 helix: -0.68 (1.07), residues: 19 sheet: 0.03 (0.60), residues: 72 loop : -1.66 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 237 TYR 0.009 0.001 TYR A 257 PHE 0.021 0.002 PHE A 159 TRP 0.007 0.001 TRP A 179 HIS 0.001 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.19 ( 1705) covalent geometry : angle 0.64891 / 0.34 ( 2337) SS BOND : bond 0.00178 / 0.10 ( 5) SS BOND : angle 3.11747 / 1.97 ( 10) hydrogen bonds : bond 0.04023 / 2.64 ( 64) hydrogen bonds : angle 5.02562 / 3.83 ( 150) link_BETA1-4 : bond 0.00331 / 0.17 ( 1) link_BETA1-4 : angle 2.07619 / 1.09 ( 3) link_NAG-ASN : bond 0.00548 / 0.28 ( 4) link_NAG-ASN : angle 3.28792 / 1.84 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 890.37 seconds wall clock time: 15 minutes 48.69 seconds (948.69 seconds total)