Starting phenix.real_space_refine on Tue Mar 3 10:50:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7usb_26731/03_2026/7usb_26731.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usb_26731/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7usb_26731/03_2026/7usb_26731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usb_26731/03_2026/7usb_26731.map" model { file = "/net/cci-nas-00/data/ceres_data/7usb_26731/03_2026/7usb_26731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usb_26731/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.65, per 1000 atoms: 0.39 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: 0.20 Conformation dependent library (CDL) restraints added in 63.4 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: 0.07 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: 0.18 Time building geometry restraints manager: 0.27 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: 992 17.81 - 35.63: 39 35.63 - 53.44: 7 53.44 - 71.25: 6 71.25 - 89.07: 1 Dihedral angle restraints: 1045 sinusoidal: 422 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 1042 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: 8.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.580 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 : 10.319 89.066 626 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 covalent geometry : bond 0.01297 ( 1705) covalent geometry : angle 1.72012 ( 2337) SS BOND : bond 0.04489 ( 5) SS BOND : angle 2.96757 ( 10) hydrogen bonds : bond 0.17079 ( 64) hydrogen bonds : angle 6.90121 ( 150) link_BETA1-4 : bond 0.00680 ( 1) link_BETA1-4 : angle 4.32483 ( 3) link_NAG-ASN : bond 0.05775 ( 4) link_NAG-ASN : angle 2.53008 ( 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 : 0.062 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.0414 time to fit residues: 1.8047 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 : 0.057 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4031 r_free = 0.4031 target = 0.180858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.153003 restraints weight = 2039.858| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.41 r_work: 0.3635 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1814 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= 0.146 Angle : 0.671 5.913 2362 Z= 0.357 Chirality : 0.049 0.257 276 Planarity : 0.004 0.031 289 Dihedral : 5.444 22.971 331 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.08 % Allowed : 4.86 % 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: -0.13 (0.54), residues: 201 helix: 1.76 (1.43), residues: 12 sheet: 1.11 (0.56), residues: 74 loop : -1.17 (0.50), residues: 115 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 0.010 0.001 PHE A 24 TRP 0.009 0.001 TRP A 88 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 1705) covalent geometry : angle 0.62664 ( 2337) SS BOND : bond 0.00721 ( 5) SS BOND : angle 0.66232 ( 10) hydrogen bonds : bond 0.05299 ( 64) hydrogen bonds : angle 5.31948 ( 150) link_BETA1-4 : bond 0.00176 ( 1) link_BETA1-4 : angle 2.61846 ( 3) link_NAG-ASN : bond 0.00455 ( 4) link_NAG-ASN : angle 3.16800 ( 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 23 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.058 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 21 average time/residue: 0.0722 time to fit residues: 1.7387 Evaluate side-chains 19 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 4 optimal weight: 0.0570 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 1 optimal weight: 0.4980 chunk 16 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.0970 chunk 2 optimal weight: 0.0770 overall best weight: 0.1254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.196490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.167437 restraints weight = 1965.923| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.46 r_work: 0.3844 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1715 Z= 0.117 Angle : 0.578 5.594 2362 Z= 0.302 Chirality : 0.047 0.237 276 Planarity : 0.003 0.030 289 Dihedral : 5.019 23.482 331 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.08 % Allowed : 6.94 % 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: -0.52 (0.54), residues: 201 helix: 1.31 (1.34), residues: 13 sheet: 0.83 (0.56), residues: 74 loop : -1.43 (0.52), 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 112 PHE 0.006 0.001 PHE A 24 TRP 0.009 0.001 TRP A 88 HIS 0.001 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 1705) covalent geometry : angle 0.53946 ( 2337) SS BOND : bond 0.00184 ( 5) SS BOND : angle 0.45222 ( 10) hydrogen bonds : bond 0.03981 ( 64) hydrogen bonds : angle 4.99197 ( 150) link_BETA1-4 : bond 0.00192 ( 1) link_BETA1-4 : angle 1.97555 ( 3) link_NAG-ASN : bond 0.00370 ( 4) link_NAG-ASN : angle 2.82356 ( 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 21 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.056 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 19 average time/residue: 0.0504 time to fit residues: 1.1738 Evaluate side-chains 19 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.056 ------------------------------------------------------------------------------- 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: 0.8980 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.181453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150424 restraints weight = 1970.590| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.56 r_work: 0.3523 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2990 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= 0.204 Angle : 0.658 6.213 2362 Z= 0.334 Chirality : 0.051 0.264 276 Planarity : 0.004 0.031 289 Dihedral : 5.611 24.071 331 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.08 % Allowed : 8.33 % Favored : 89.58 % 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: -0.97 (0.56), residues: 201 helix: 0.80 (1.27), residues: 13 sheet: 0.44 (0.60), residues: 73 loop : -1.63 (0.52), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 154 TYR 0.008 0.001 TYR A 112 PHE 0.010 0.002 PHE A 59 TRP 0.007 0.001 TRP A 88 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 1705) covalent geometry : angle 0.60672 ( 2337) SS BOND : bond 0.00625 ( 5) SS BOND : angle 0.63212 ( 10) hydrogen bonds : bond 0.04142 ( 64) hydrogen bonds : angle 5.04127 ( 150) link_BETA1-4 : bond 0.00217 ( 1) link_BETA1-4 : angle 2.38089 ( 3) link_NAG-ASN : bond 0.00429 ( 4) link_NAG-ASN : angle 3.44873 ( 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 : 0.065 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 21 average time/residue: 0.0592 time to fit residues: 1.4682 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 : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASN 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: 0.1980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 0 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.0870 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.180004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.148978 restraints weight = 2002.785| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.57 r_work: 0.3510 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 1715 Z= 0.200 Angle : 0.661 6.497 2362 Z= 0.331 Chirality : 0.051 0.263 276 Planarity : 0.004 0.032 289 Dihedral : 5.818 24.640 331 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.47 % Allowed : 9.03 % 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: -1.10 (0.56), residues: 201 helix: 0.79 (1.30), residues: 13 sheet: 0.28 (0.61), residues: 73 loop : -1.67 (0.53), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 46 TYR 0.006 0.001 TYR A 58 PHE 0.017 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 covalent geometry : bond 0.00484 ( 1705) covalent geometry : angle 0.60871 ( 2337) SS BOND : bond 0.00330 ( 5) SS BOND : angle 0.82981 ( 10) hydrogen bonds : bond 0.03991 ( 64) hydrogen bonds : angle 5.04686 ( 150) link_BETA1-4 : bond 0.00336 ( 1) link_BETA1-4 : angle 2.35159 ( 3) link_NAG-ASN : bond 0.00491 ( 4) link_NAG-ASN : angle 3.44518 ( 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 24 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.063 Fit side-chains revert: symmetry clash REVERT: A 240 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7971 (t0) outliers start: 5 outliers final: 4 residues processed: 22 average time/residue: 0.0587 time to fit residues: 1.5307 Evaluate side-chains 23 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.078 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 240 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 0.1980 chunk 1 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.0870 chunk 2 optimal weight: 0.0050 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.0060 overall best weight: 0.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.173742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.143159 restraints weight = 1957.117| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.52 r_work: 0.3545 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 1715 Z= 0.097 Angle : 0.551 5.641 2362 Z= 0.284 Chirality : 0.047 0.233 276 Planarity : 0.003 0.029 289 Dihedral : 5.378 23.996 331 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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: -0.98 (0.57), residues: 201 helix: 1.02 (1.32), residues: 13 sheet: 0.21 (0.60), residues: 74 loop : -1.50 (0.55), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 237 TYR 0.005 0.001 TYR A 112 PHE 0.019 0.001 PHE A 159 TRP 0.008 0.001 TRP A 88 HIS 0.001 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 1705) covalent geometry : angle 0.51140 ( 2337) SS BOND : bond 0.00155 ( 5) SS BOND : angle 0.53754 ( 10) hydrogen bonds : bond 0.03562 ( 64) hydrogen bonds : angle 4.85437 ( 150) link_BETA1-4 : bond 0.00130 ( 1) link_BETA1-4 : angle 1.86682 ( 3) link_NAG-ASN : bond 0.00366 ( 4) link_NAG-ASN : angle 2.79382 ( 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 27 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.063 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.0584 time to fit residues: 1.7237 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 1 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 2 optimal weight: 0.3980 chunk 20 optimal weight: 0.0870 chunk 12 optimal weight: 0.4980 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.171128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.140722 restraints weight = 1960.738| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.50 r_work: 0.3514 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1715 Z= 0.167 Angle : 0.616 5.966 2362 Z= 0.311 Chirality : 0.049 0.252 276 Planarity : 0.003 0.028 289 Dihedral : 5.556 24.905 331 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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: -1.13 (0.58), residues: 201 helix: 0.95 (1.32), residues: 13 sheet: 0.14 (0.62), residues: 73 loop : -1.61 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 46 TYR 0.005 0.001 TYR A 112 PHE 0.006 0.001 PHE A 159 TRP 0.008 0.001 TRP A 88 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 1705) covalent geometry : angle 0.56940 ( 2337) SS BOND : bond 0.00309 ( 5) SS BOND : angle 0.48659 ( 10) hydrogen bonds : bond 0.03807 ( 64) hydrogen bonds : angle 4.94640 ( 150) link_BETA1-4 : bond 0.00178 ( 1) link_BETA1-4 : angle 2.19467 ( 3) link_NAG-ASN : bond 0.00437 ( 4) link_NAG-ASN : angle 3.18589 ( 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 26 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.062 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.0428 time to fit residues: 1.2404 Evaluate side-chains 25 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.058 ------------------------------------------------------------------------------- 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: 0.0870 chunk 10 optimal weight: 0.0570 chunk 11 optimal weight: 0.3980 chunk 2 optimal weight: 0.0370 chunk 18 optimal weight: 0.3980 chunk 8 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 1 optimal weight: 0.1980 chunk 17 optimal weight: 0.2980 chunk 20 optimal weight: 0.3980 overall best weight: 0.0752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3985 r_free = 0.3985 target = 0.174655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.144481 restraints weight = 1966.818| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.49 r_work: 0.3582 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 1715 Z= 0.096 Angle : 0.523 4.929 2362 Z= 0.273 Chirality : 0.046 0.217 276 Planarity : 0.003 0.028 289 Dihedral : 5.086 24.252 331 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.08 % Allowed : 11.11 % 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: -1.07 (0.58), residues: 201 helix: 1.15 (1.33), residues: 13 sheet: -0.09 (0.61), residues: 76 loop : -1.41 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 237 TYR 0.005 0.001 TYR A 43 PHE 0.003 0.001 PHE A 197 TRP 0.008 0.001 TRP A 88 HIS 0.001 0.000 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 1705) covalent geometry : angle 0.49051 ( 2337) SS BOND : bond 0.00128 ( 5) SS BOND : angle 0.60454 ( 10) hydrogen bonds : bond 0.03257 ( 64) hydrogen bonds : angle 4.70940 ( 150) link_BETA1-4 : bond 0.00195 ( 1) link_BETA1-4 : angle 1.73930 ( 3) link_NAG-ASN : bond 0.00368 ( 4) link_NAG-ASN : angle 2.43011 ( 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 24 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.061 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.0539 time to fit residues: 1.3966 Evaluate side-chains 24 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.055 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 0 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.0970 chunk 7 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3942 r_free = 0.3942 target = 0.170524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140043 restraints weight = 2003.329| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.52 r_work: 0.3512 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1715 Z= 0.185 Angle : 0.617 5.815 2362 Z= 0.310 Chirality : 0.050 0.250 276 Planarity : 0.003 0.029 289 Dihedral : 5.551 25.006 331 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % 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: -1.21 (0.58), residues: 201 helix: 1.01 (1.33), residues: 13 sheet: 0.04 (0.62), residues: 73 loop : -1.65 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 46 TYR 0.006 0.001 TYR A 58 PHE 0.006 0.001 PHE A 59 TRP 0.007 0.001 TRP A 88 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 1705) covalent geometry : angle 0.56973 ( 2337) SS BOND : bond 0.00305 ( 5) SS BOND : angle 0.50698 ( 10) hydrogen bonds : bond 0.03816 ( 64) hydrogen bonds : angle 4.93817 ( 150) link_BETA1-4 : bond 0.00209 ( 1) link_BETA1-4 : angle 2.24950 ( 3) link_NAG-ASN : bond 0.00440 ( 4) link_NAG-ASN : angle 3.21318 ( 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 26 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.055 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.0517 time to fit residues: 1.4865 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 : 0.055 ------------------------------------------------------------------------------- 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: 0.2980 chunk 18 optimal weight: 0.1980 chunk 14 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 0.0980 chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 8 optimal weight: 0.0980 chunk 17 optimal weight: 0.4980 chunk 6 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 overall best weight: 0.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3967 r_free = 0.3967 target = 0.172404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.142628 restraints weight = 1956.133| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.49 r_work: 0.3740 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 1715 Z= 0.151 Angle : 0.759 14.644 2362 Z= 0.380 Chirality : 0.047 0.238 276 Planarity : 0.003 0.029 289 Dihedral : 5.653 24.162 331 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.18 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: -1.45 (0.57), residues: 201 helix: 1.01 (1.32), residues: 13 sheet: -0.19 (0.62), residues: 76 loop : -1.83 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 237 TYR 0.005 0.001 TYR A 257 PHE 0.003 0.001 PHE A 180 TRP 0.007 0.001 TRP A 88 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 1705) covalent geometry : angle 0.66310 ( 2337) SS BOND : bond 0.00160 ( 5) SS BOND : angle 4.55697 ( 10) hydrogen bonds : bond 0.03498 ( 64) hydrogen bonds : angle 4.84994 ( 150) link_BETA1-4 : bond 0.00153 ( 1) link_BETA1-4 : angle 2.03461 ( 3) link_NAG-ASN : bond 0.00861 ( 4) link_NAG-ASN : angle 3.04518 ( 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 30 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.050 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.0415 time to fit residues: 1.3857 Evaluate side-chains 27 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.033 ------------------------------------------------------------------------------- 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: 0.9980 chunk 7 optimal weight: 0.4980 chunk 9 optimal weight: 0.0670 chunk 10 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 6 optimal weight: 0.0870 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 0.0870 chunk 19 optimal weight: 0.5980 overall best weight: 0.1452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3961 r_free = 0.3961 target = 0.173487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.144289 restraints weight = 2007.927| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.49 r_work: 0.3535 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 1715 Z= 0.143 Angle : 0.681 10.962 2362 Z= 0.346 Chirality : 0.047 0.232 276 Planarity : 0.003 0.028 289 Dihedral : 5.647 27.630 331 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.08 % Allowed : 12.50 % Favored : 85.42 % 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: -1.41 (0.57), residues: 201 helix: 1.22 (1.33), residues: 13 sheet: -0.20 (0.61), residues: 76 loop : -1.78 (0.54), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 46 TYR 0.007 0.001 TYR A 257 PHE 0.003 0.001 PHE A 180 TRP 0.007 0.001 TRP A 149 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 1705) covalent geometry : angle 0.61010 ( 2337) SS BOND : bond 0.00115 ( 5) SS BOND : angle 3.44825 ( 10) hydrogen bonds : bond 0.03633 ( 64) hydrogen bonds : angle 4.84163 ( 150) link_BETA1-4 : bond 0.00165 ( 1) link_BETA1-4 : angle 1.53970 ( 3) link_NAG-ASN : bond 0.00628 ( 4) link_NAG-ASN : angle 2.86799 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 924.26 seconds wall clock time: 16 minutes 26.85 seconds (986.85 seconds total)