Starting phenix.real_space_refine on Wed Sep 17 03:00:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dbe_46716/09_2025/9dbe_46716.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dbe_46716/09_2025/9dbe_46716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dbe_46716/09_2025/9dbe_46716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dbe_46716/09_2025/9dbe_46716.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dbe_46716/09_2025/9dbe_46716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dbe_46716/09_2025/9dbe_46716.map" } resolution = 2.4 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= 0.060 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 9 5.16 5 C 1348 2.51 5 N 336 2.21 5 O 457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2150 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1920 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 237} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 6, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 60 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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 Chain: "G" 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: 29, 42 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1, 'water': 28} Link IDs: {None: 28} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.87, per 1000 atoms: 0.40 Number of scatterers: 2150 At special positions: 0 Unit cell: (66.5016, 65.494, 65.494, 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 9 16.00 O 457 8.00 N 336 7.00 C 1348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 68 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 160 " distance=2.04 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 260 " distance=2.04 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 3 " NAG-ASN " NAG A1501 " - " ASN A 236 " " NAG B 1 " - " ASN A 176 " " NAG C 1 " - " ASN A 210 " " NAG D 1 " - " ASN A 243 " " NAG E 1 " - " ASN A 29 " " NAG F 1 " - " ASN A 95 " " NAG G 1 " - " ASN A 67 " Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 78.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 458 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 11.0% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 38 through 45 removed outlier: 3.662A pdb=" N PHE A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.831A pdb=" N CYS A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 58 removed outlier: 4.561A pdb=" N TYR A 239 " --> pdb=" O CYS A 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 81 removed outlier: 6.943A pdb=" N ALA A 76 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE A 208 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N GLU A 112 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASN A 210 " --> pdb=" O HIS A 110 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 106 " --> pdb=" O MET A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 202 76 hydrogen bonds defined for protein. 192 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: 0.29 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 621 1.34 - 1.46: 577 1.46 - 1.58: 967 1.58 - 1.70: 0 1.70 - 1.82: 12 Bond restraints: 2177 Sorted by residual: bond pdb=" C VAL A 167 " pdb=" O VAL A 167 " ideal model delta sigma weight residual 1.232 1.240 -0.009 1.01e-02 9.80e+03 7.22e-01 bond pdb=" N VAL A 167 " pdb=" CA VAL A 167 " ideal model delta sigma weight residual 1.456 1.461 -0.005 8.60e-03 1.35e+04 3.14e-01 bond pdb=" C VAL A 171 " pdb=" N ILE A 172 " ideal model delta sigma weight residual 1.329 1.324 0.006 1.13e-02 7.83e+03 2.45e-01 bond pdb=" C LYS A 166 " pdb=" N VAL A 167 " ideal model delta sigma weight residual 1.326 1.330 -0.004 9.20e-03 1.18e+04 2.32e-01 bond pdb=" CA THR A 238 " pdb=" CB THR A 238 " ideal model delta sigma weight residual 1.533 1.544 -0.011 2.29e-02 1.91e+03 2.28e-01 ... (remaining 2172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 2851 1.28 - 2.56: 105 2.56 - 3.84: 16 3.84 - 5.12: 2 5.12 - 6.39: 1 Bond angle restraints: 2975 Sorted by residual: angle pdb=" N VAL A 171 " pdb=" CA VAL A 171 " pdb=" C VAL A 171 " ideal model delta sigma weight residual 109.34 104.79 4.55 2.08e+00 2.31e-01 4.78e+00 angle pdb=" C GLN A 128 " pdb=" N HIS A 129 " pdb=" CA HIS A 129 " ideal model delta sigma weight residual 121.54 125.23 -3.69 1.91e+00 2.74e-01 3.73e+00 angle pdb=" CA CYS A 260 " pdb=" CB CYS A 260 " pdb=" SG CYS A 260 " ideal model delta sigma weight residual 114.40 118.75 -4.35 2.30e+00 1.89e-01 3.58e+00 angle pdb=" N VAL A 167 " pdb=" CA VAL A 167 " pdb=" C VAL A 167 " ideal model delta sigma weight residual 108.15 109.98 -1.83 9.90e-01 1.02e+00 3.43e+00 angle pdb=" N GLY A 182 " pdb=" CA GLY A 182 " pdb=" C GLY A 182 " ideal model delta sigma weight residual 111.14 114.37 -3.23 1.80e+00 3.09e-01 3.21e+00 ... (remaining 2970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.10: 1286 12.10 - 24.19: 94 24.19 - 36.29: 41 36.29 - 48.38: 11 48.38 - 60.48: 4 Dihedral angle restraints: 1436 sinusoidal: 715 harmonic: 721 Sorted by residual: dihedral pdb=" CA SER A 170 " pdb=" C SER A 170 " pdb=" N VAL A 171 " pdb=" CA VAL A 171 " ideal model delta harmonic sigma weight residual 180.00 157.03 22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA TRP A 185 " pdb=" C TRP A 185 " pdb=" N ASN A 186 " pdb=" CA ASN A 186 " ideal model delta harmonic sigma weight residual 180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA TYR A 229 " pdb=" C TYR A 229 " pdb=" N VAL A 230 " pdb=" CA VAL A 230 " ideal model delta harmonic sigma weight residual 180.00 164.82 15.18 0 5.00e+00 4.00e-02 9.22e+00 ... (remaining 1433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 202 0.029 - 0.058: 97 0.058 - 0.086: 40 0.086 - 0.115: 23 0.115 - 0.144: 7 Chirality restraints: 369 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 176 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA VAL A 171 " pdb=" N VAL A 171 " pdb=" C VAL A 171 " pdb=" CB VAL A 171 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 67 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 366 not shown) Planarity restraints: 365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 112 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.36e+00 pdb=" N PRO A 113 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 103 " -0.016 5.00e-02 4.00e+02 2.37e-02 9.02e-01 pdb=" N PRO A 104 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 107 " 0.008 2.00e-02 2.50e+03 6.80e-03 8.09e-01 pdb=" CG PHE A 107 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE A 107 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 107 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 107 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 107 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 107 " 0.003 2.00e-02 2.50e+03 ... (remaining 362 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 430 2.79 - 3.31: 1715 3.31 - 3.84: 3507 3.84 - 4.37: 4272 4.37 - 4.90: 7090 Nonbonded interactions: 17014 Sorted by model distance: nonbonded pdb=" OG SER A 170 " pdb=" O VAL A 171 " model vdw 2.258 3.040 nonbonded pdb=" O5 NAG D 2 " pdb=" O6 NAG D 2 " model vdw 2.443 2.432 nonbonded pdb=" O5 NAG E 1 " pdb=" O6 NAG E 1 " model vdw 2.505 2.432 nonbonded pdb=" N VAL A 171 " pdb=" O VAL A 171 " model vdw 2.545 2.496 nonbonded pdb=" O ALA A 122 " pdb=" NH2 ARG A 130 " model vdw 2.565 3.120 ... (remaining 17009 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.540 Find NCS groups from input model: 0.020 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.003 0.022 2195 Z= 0.136 Angle : 0.622 6.395 3026 Z= 0.316 Chirality : 0.045 0.144 369 Planarity : 0.003 0.029 358 Dihedral : 10.735 60.479 969 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.51 % Allowed : 5.53 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 0.06 (0.53), residues: 243 helix: -1.84 (1.16), residues: 14 sheet: 0.96 (0.49), residues: 96 loop : -0.41 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 217 TYR 0.008 0.001 TYR A 240 PHE 0.015 0.002 PHE A 107 TRP 0.005 0.001 TRP A 207 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 2177) covalent geometry : angle 0.58906 ( 2975) SS BOND : bond 0.00640 ( 3) SS BOND : angle 0.74902 ( 6) hydrogen bonds : bond 0.14064 ( 76) hydrogen bonds : angle 6.19963 ( 192) link_BETA1-4 : bond 0.00372 ( 6) link_BETA1-4 : angle 1.66602 ( 18) link_BETA1-6 : bond 0.00344 ( 2) link_BETA1-6 : angle 1.13384 ( 6) link_NAG-ASN : bond 0.00302 ( 7) link_NAG-ASN : angle 1.92970 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.089 Fit side-chains REVERT: A 231 TYR cc_start: 0.9286 (OUTLIER) cc_final: 0.8821 (p90) outliers start: 3 outliers final: 1 residues processed: 34 average time/residue: 0.7244 time to fit residues: 25.0570 Evaluate side-chains 30 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 231 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 36 ASN A 135 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.106132 restraints weight = 2209.247| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.68 r_work: 0.3043 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2195 Z= 0.177 Angle : 0.684 6.408 3026 Z= 0.348 Chirality : 0.048 0.148 369 Planarity : 0.004 0.029 358 Dihedral : 6.931 44.477 579 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.02 % Allowed : 11.06 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 0.05 (0.53), residues: 243 helix: -2.16 (1.13), residues: 14 sheet: 0.92 (0.47), residues: 103 loop : -0.42 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 217 TYR 0.010 0.002 TYR A 215 PHE 0.015 0.002 PHE A 107 TRP 0.006 0.002 TRP A 207 HIS 0.002 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 2177) covalent geometry : angle 0.65154 ( 2975) SS BOND : bond 0.00530 ( 3) SS BOND : angle 0.79422 ( 6) hydrogen bonds : bond 0.05694 ( 76) hydrogen bonds : angle 5.84947 ( 192) link_BETA1-4 : bond 0.00458 ( 6) link_BETA1-4 : angle 1.75321 ( 18) link_BETA1-6 : bond 0.00358 ( 2) link_BETA1-6 : angle 1.08260 ( 6) link_NAG-ASN : bond 0.00394 ( 7) link_NAG-ASN : angle 2.03462 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.083 Fit side-chains REVERT: A 231 TYR cc_start: 0.9300 (OUTLIER) cc_final: 0.8806 (p90) REVERT: A 237 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8591 (t80) outliers start: 6 outliers final: 2 residues processed: 33 average time/residue: 0.7387 time to fit residues: 24.7958 Evaluate side-chains 33 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 14 optimal weight: 0.0370 chunk 2 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.129337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.108513 restraints weight = 2180.896| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.59 r_work: 0.3077 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2195 Z= 0.109 Angle : 0.585 6.189 3026 Z= 0.295 Chirality : 0.045 0.135 369 Planarity : 0.003 0.026 358 Dihedral : 6.206 44.394 579 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.51 % Allowed : 12.06 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 0.14 (0.54), residues: 243 helix: -2.01 (1.10), residues: 14 sheet: 0.93 (0.49), residues: 100 loop : -0.29 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 217 TYR 0.012 0.001 TYR A 215 PHE 0.015 0.002 PHE A 107 TRP 0.004 0.001 TRP A 207 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 2177) covalent geometry : angle 0.55057 ( 2975) SS BOND : bond 0.00445 ( 3) SS BOND : angle 0.85739 ( 6) hydrogen bonds : bond 0.04622 ( 76) hydrogen bonds : angle 5.75158 ( 192) link_BETA1-4 : bond 0.00383 ( 6) link_BETA1-4 : angle 1.67399 ( 18) link_BETA1-6 : bond 0.00384 ( 2) link_BETA1-6 : angle 1.11585 ( 6) link_NAG-ASN : bond 0.00270 ( 7) link_NAG-ASN : angle 1.82869 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.094 Fit side-chains REVERT: A 231 TYR cc_start: 0.9286 (OUTLIER) cc_final: 0.8808 (p90) REVERT: A 237 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8457 (t80) outliers start: 3 outliers final: 0 residues processed: 32 average time/residue: 0.7740 time to fit residues: 25.2433 Evaluate side-chains 29 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.107025 restraints weight = 2176.026| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.60 r_work: 0.3058 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2195 Z= 0.147 Angle : 0.630 6.371 3026 Z= 0.319 Chirality : 0.046 0.144 369 Planarity : 0.004 0.028 358 Dihedral : 6.227 45.302 578 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.51 % Allowed : 13.07 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 0.16 (0.53), residues: 243 helix: -1.95 (1.15), residues: 14 sheet: 0.97 (0.49), residues: 100 loop : -0.32 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 217 TYR 0.012 0.002 TYR A 215 PHE 0.015 0.002 PHE A 107 TRP 0.005 0.001 TRP A 207 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 2177) covalent geometry : angle 0.59587 ( 2975) SS BOND : bond 0.00445 ( 3) SS BOND : angle 0.82700 ( 6) hydrogen bonds : bond 0.05059 ( 76) hydrogen bonds : angle 5.80127 ( 192) link_BETA1-4 : bond 0.00428 ( 6) link_BETA1-4 : angle 1.70067 ( 18) link_BETA1-6 : bond 0.00485 ( 2) link_BETA1-6 : angle 1.07512 ( 6) link_NAG-ASN : bond 0.00333 ( 7) link_NAG-ASN : angle 1.94824 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.078 Fit side-chains REVERT: A 231 TYR cc_start: 0.9308 (OUTLIER) cc_final: 0.8773 (p90) REVERT: A 237 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8534 (t80) outliers start: 5 outliers final: 1 residues processed: 31 average time/residue: 0.7643 time to fit residues: 24.1141 Evaluate side-chains 29 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.107099 restraints weight = 2153.946| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.63 r_work: 0.3057 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2195 Z= 0.147 Angle : 0.632 6.635 3026 Z= 0.320 Chirality : 0.046 0.144 369 Planarity : 0.004 0.028 358 Dihedral : 6.189 45.616 578 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.02 % Allowed : 12.56 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 0.17 (0.54), residues: 243 helix: -1.89 (1.13), residues: 14 sheet: 1.08 (0.49), residues: 98 loop : -0.38 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 217 TYR 0.012 0.001 TYR A 215 PHE 0.015 0.002 PHE A 107 TRP 0.005 0.001 TRP A 207 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 2177) covalent geometry : angle 0.59856 ( 2975) SS BOND : bond 0.00448 ( 3) SS BOND : angle 0.75365 ( 6) hydrogen bonds : bond 0.05036 ( 76) hydrogen bonds : angle 5.81720 ( 192) link_BETA1-4 : bond 0.00415 ( 6) link_BETA1-4 : angle 1.69360 ( 18) link_BETA1-6 : bond 0.00447 ( 2) link_BETA1-6 : angle 1.09916 ( 6) link_NAG-ASN : bond 0.00327 ( 7) link_NAG-ASN : angle 1.95597 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.082 Fit side-chains REVERT: A 231 TYR cc_start: 0.9311 (OUTLIER) cc_final: 0.8801 (p90) REVERT: A 237 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8538 (t80) outliers start: 6 outliers final: 1 residues processed: 33 average time/residue: 0.6941 time to fit residues: 23.3213 Evaluate side-chains 31 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.127975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107454 restraints weight = 2152.158| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.56 r_work: 0.3064 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2195 Z= 0.144 Angle : 0.628 6.760 3026 Z= 0.318 Chirality : 0.046 0.145 369 Planarity : 0.004 0.027 358 Dihedral : 6.148 45.758 578 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.52 % Allowed : 11.56 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 0.17 (0.54), residues: 243 helix: -1.89 (1.13), residues: 14 sheet: 1.09 (0.49), residues: 98 loop : -0.39 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 217 TYR 0.011 0.001 TYR A 215 PHE 0.015 0.002 PHE A 107 TRP 0.005 0.001 TRP A 185 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 2177) covalent geometry : angle 0.59388 ( 2975) SS BOND : bond 0.00510 ( 3) SS BOND : angle 0.88080 ( 6) hydrogen bonds : bond 0.04981 ( 76) hydrogen bonds : angle 5.81249 ( 192) link_BETA1-4 : bond 0.00414 ( 6) link_BETA1-4 : angle 1.69091 ( 18) link_BETA1-6 : bond 0.00457 ( 2) link_BETA1-6 : angle 1.09930 ( 6) link_NAG-ASN : bond 0.00326 ( 7) link_NAG-ASN : angle 1.95338 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.082 Fit side-chains REVERT: A 231 TYR cc_start: 0.9317 (OUTLIER) cc_final: 0.8742 (p90) REVERT: A 237 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8542 (t80) outliers start: 7 outliers final: 1 residues processed: 35 average time/residue: 0.6794 time to fit residues: 24.2050 Evaluate side-chains 30 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.127683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.106690 restraints weight = 2156.615| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.59 r_work: 0.3051 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2195 Z= 0.173 Angle : 0.669 7.117 3026 Z= 0.339 Chirality : 0.047 0.150 369 Planarity : 0.004 0.028 358 Dihedral : 6.302 46.333 578 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.02 % Allowed : 12.06 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 0.15 (0.53), residues: 243 helix: -1.98 (1.14), residues: 14 sheet: 1.02 (0.49), residues: 100 loop : -0.37 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 217 TYR 0.011 0.002 TYR A 215 PHE 0.015 0.002 PHE A 107 TRP 0.006 0.002 TRP A 185 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 2177) covalent geometry : angle 0.63628 ( 2975) SS BOND : bond 0.00541 ( 3) SS BOND : angle 0.89610 ( 6) hydrogen bonds : bond 0.05330 ( 76) hydrogen bonds : angle 5.84673 ( 192) link_BETA1-4 : bond 0.00450 ( 6) link_BETA1-4 : angle 1.72754 ( 18) link_BETA1-6 : bond 0.00432 ( 2) link_BETA1-6 : angle 1.10999 ( 6) link_NAG-ASN : bond 0.00367 ( 7) link_NAG-ASN : angle 2.02282 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.072 Fit side-chains REVERT: A 213 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9184 (tp) REVERT: A 231 TYR cc_start: 0.9311 (OUTLIER) cc_final: 0.8760 (p90) REVERT: A 237 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8601 (t80) outliers start: 6 outliers final: 1 residues processed: 33 average time/residue: 0.6951 time to fit residues: 23.3383 Evaluate side-chains 31 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.106830 restraints weight = 2170.498| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.57 r_work: 0.3053 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2195 Z= 0.169 Angle : 0.664 7.256 3026 Z= 0.336 Chirality : 0.047 0.149 369 Planarity : 0.004 0.028 358 Dihedral : 6.306 46.432 578 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.51 % Allowed : 12.56 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 0.14 (0.53), residues: 243 helix: -2.05 (1.12), residues: 14 sheet: 0.99 (0.49), residues: 100 loop : -0.33 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 217 TYR 0.011 0.002 TYR A 215 PHE 0.015 0.002 PHE A 107 TRP 0.006 0.002 TRP A 185 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 2177) covalent geometry : angle 0.63076 ( 2975) SS BOND : bond 0.00520 ( 3) SS BOND : angle 0.85194 ( 6) hydrogen bonds : bond 0.05283 ( 76) hydrogen bonds : angle 5.85115 ( 192) link_BETA1-4 : bond 0.00440 ( 6) link_BETA1-4 : angle 1.73038 ( 18) link_BETA1-6 : bond 0.00432 ( 2) link_BETA1-6 : angle 1.10270 ( 6) link_NAG-ASN : bond 0.00371 ( 7) link_NAG-ASN : angle 2.02992 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.048 Fit side-chains REVERT: A 213 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9190 (tp) REVERT: A 231 TYR cc_start: 0.9310 (OUTLIER) cc_final: 0.8769 (p90) REVERT: A 237 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8599 (t80) outliers start: 5 outliers final: 1 residues processed: 32 average time/residue: 0.7235 time to fit residues: 23.4925 Evaluate side-chains 30 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.106507 restraints weight = 2187.086| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.61 r_work: 0.3050 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2195 Z= 0.162 Angle : 0.657 7.190 3026 Z= 0.332 Chirality : 0.047 0.148 369 Planarity : 0.004 0.028 358 Dihedral : 6.287 46.494 578 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.02 % Allowed : 11.56 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 0.13 (0.53), residues: 243 helix: -2.08 (1.10), residues: 14 sheet: 0.99 (0.49), residues: 100 loop : -0.36 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 217 TYR 0.011 0.002 TYR A 215 PHE 0.015 0.002 PHE A 107 TRP 0.006 0.002 TRP A 185 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 2177) covalent geometry : angle 0.62308 ( 2975) SS BOND : bond 0.00499 ( 3) SS BOND : angle 0.77150 ( 6) hydrogen bonds : bond 0.05218 ( 76) hydrogen bonds : angle 5.84311 ( 192) link_BETA1-4 : bond 0.00434 ( 6) link_BETA1-4 : angle 1.72568 ( 18) link_BETA1-6 : bond 0.00436 ( 2) link_BETA1-6 : angle 1.09992 ( 6) link_NAG-ASN : bond 0.00360 ( 7) link_NAG-ASN : angle 2.02664 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.081 Fit side-chains REVERT: A 213 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9182 (tp) REVERT: A 231 TYR cc_start: 0.9309 (OUTLIER) cc_final: 0.8771 (p90) REVERT: A 237 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8590 (t80) outliers start: 8 outliers final: 2 residues processed: 33 average time/residue: 0.5842 time to fit residues: 19.6177 Evaluate side-chains 31 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.126850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.105781 restraints weight = 2198.500| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.60 r_work: 0.3038 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2195 Z= 0.205 Angle : 0.719 7.596 3026 Z= 0.363 Chirality : 0.049 0.157 369 Planarity : 0.004 0.030 358 Dihedral : 6.525 46.923 578 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.02 % Allowed : 11.56 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 0.02 (0.53), residues: 243 helix: -2.28 (1.04), residues: 14 sheet: 0.98 (0.48), residues: 100 loop : -0.47 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 217 TYR 0.010 0.002 TYR A 231 PHE 0.015 0.003 PHE A 107 TRP 0.007 0.002 TRP A 185 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 2177) covalent geometry : angle 0.68635 ( 2975) SS BOND : bond 0.00606 ( 3) SS BOND : angle 0.87020 ( 6) hydrogen bonds : bond 0.05685 ( 76) hydrogen bonds : angle 5.89084 ( 192) link_BETA1-4 : bond 0.00487 ( 6) link_BETA1-4 : angle 1.79405 ( 18) link_BETA1-6 : bond 0.00424 ( 2) link_BETA1-6 : angle 1.11238 ( 6) link_NAG-ASN : bond 0.00417 ( 7) link_NAG-ASN : angle 2.10091 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.091 Fit side-chains REVERT: A 213 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9131 (tp) REVERT: A 231 TYR cc_start: 0.9319 (OUTLIER) cc_final: 0.8724 (p90) REVERT: A 237 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8638 (t80) outliers start: 8 outliers final: 3 residues processed: 35 average time/residue: 0.6111 time to fit residues: 21.8122 Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 0.0870 chunk 20 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.1980 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 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108081 restraints weight = 2179.529| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.60 r_work: 0.3074 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2195 Z= 0.114 Angle : 0.600 6.722 3026 Z= 0.302 Chirality : 0.045 0.142 369 Planarity : 0.003 0.027 358 Dihedral : 5.938 46.227 578 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.02 % Allowed : 12.56 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 aren not related in a simple way. whole: 0.19 (0.54), residues: 243 helix: -1.80 (1.14), residues: 14 sheet: 1.00 (0.49), residues: 100 loop : -0.31 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.011 0.001 TYR A 215 PHE 0.015 0.002 PHE A 107 TRP 0.005 0.001 TRP A 201 HIS 0.001 0.000 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 2177) covalent geometry : angle 0.56452 ( 2975) SS BOND : bond 0.00493 ( 3) SS BOND : angle 0.80298 ( 6) hydrogen bonds : bond 0.04566 ( 76) hydrogen bonds : angle 5.81211 ( 192) link_BETA1-4 : bond 0.00379 ( 6) link_BETA1-4 : angle 1.67611 ( 18) link_BETA1-6 : bond 0.00473 ( 2) link_BETA1-6 : angle 1.09132 ( 6) link_NAG-ASN : bond 0.00282 ( 7) link_NAG-ASN : angle 1.95807 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1278.03 seconds wall clock time: 22 minutes 33.02 seconds (1353.02 seconds total)