Starting phenix.real_space_refine on Wed Jun 4 11:18:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bt9_44884/06_2025/9bt9_44884.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bt9_44884/06_2025/9bt9_44884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bt9_44884/06_2025/9bt9_44884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bt9_44884/06_2025/9bt9_44884.map" model { file = "/net/cci-nas-00/data/ceres_data/9bt9_44884/06_2025/9bt9_44884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bt9_44884/06_2025/9bt9_44884.cif" } resolution = 2.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.002 sd= 0.065 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 8 5.16 5 C 1526 2.51 5 N 356 2.21 5 O 475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 2365 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2192 Classifications: {'peptide': 268} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 258} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.28, per 1000 atoms: 1.39 Number of scatterers: 2365 At special positions: 0 Unit cell: (64.7215, 54.8335, 80.9018, 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 8 16.00 O 475 8.00 N 356 7.00 C 1526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.04 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1401 " - " ASN A 29 " " NAG A1402 " - " ASN A 58 " " NAG A1403 " - " ASN A 192 " " NAG A1404 " - " ASN A 251 " " NAG B 1 " - " ASN A 19 " " NAG C 1 " - " ASN A 132 " " NAG D 1 " - " ASN A 188 " Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 331.3 milliseconds 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 508 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 6 sheets defined 1.5% alpha, 44.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.848A pdb=" N GLN A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 39 removed outlier: 3.962A pdb=" N ARG A 34 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N PHE A 74 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ASN A 73 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY A 101 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE A 209 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 225 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 68 removed outlier: 3.605A pdb=" N ASN A 278 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.993A pdb=" N THR A 241 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N TRP A 174 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.528A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 109 through 113 69 hydrogen bonds defined for protein. 177 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: 0.65 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 620 1.33 - 1.45: 499 1.45 - 1.57: 1300 1.57 - 1.69: 0 1.69 - 1.81: 10 Bond restraints: 2429 Sorted by residual: bond pdb=" CZ ARG A 170 " pdb=" NH2 ARG A 170 " ideal model delta sigma weight residual 1.330 1.281 0.049 1.30e-02 5.92e+03 1.42e+01 bond pdb=" C3 BMA C 3 " pdb=" O3 BMA C 3 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C5 NAG A1401 " pdb=" O5 NAG A1401 " ideal model delta sigma weight residual 1.413 1.485 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C5 NAG A1403 " pdb=" O5 NAG A1403 " ideal model delta sigma weight residual 1.413 1.483 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 2424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 2095 1.44 - 2.87: 927 2.87 - 4.31: 252 4.31 - 5.74: 28 5.74 - 7.18: 9 Bond angle restraints: 3311 Sorted by residual: angle pdb=" N CYS A 151 " pdb=" CA CYS A 151 " pdb=" C CYS A 151 " ideal model delta sigma weight residual 111.71 118.69 -6.98 1.34e+00 5.57e-01 2.71e+01 angle pdb=" CA PHE A 121 " pdb=" CB PHE A 121 " pdb=" CG PHE A 121 " ideal model delta sigma weight residual 113.80 118.71 -4.91 1.00e+00 1.00e+00 2.41e+01 angle pdb=" CB HIS A 234 " pdb=" CG HIS A 234 " pdb=" CD2 HIS A 234 " ideal model delta sigma weight residual 131.20 125.01 6.19 1.30e+00 5.92e-01 2.27e+01 angle pdb=" CB HIS A 175 " pdb=" CG HIS A 175 " pdb=" CD2 HIS A 175 " ideal model delta sigma weight residual 131.20 125.14 6.06 1.30e+00 5.92e-01 2.17e+01 angle pdb=" CB HIS A 201 " pdb=" CG HIS A 201 " pdb=" CD2 HIS A 201 " ideal model delta sigma weight residual 131.20 125.49 5.71 1.30e+00 5.92e-01 1.93e+01 ... (remaining 3306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.26: 1481 20.26 - 40.52: 67 40.52 - 60.78: 7 60.78 - 81.04: 6 81.04 - 101.30: 8 Dihedral angle restraints: 1569 sinusoidal: 770 harmonic: 799 Sorted by residual: dihedral pdb=" CA ALA A 150 " pdb=" C ALA A 150 " pdb=" N CYS A 151 " pdb=" CA CYS A 151 " ideal model delta harmonic sigma weight residual -180.00 -152.01 -27.99 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA VAL A 113 " pdb=" C VAL A 113 " pdb=" N ASN A 114 " pdb=" CA ASN A 114 " ideal model delta harmonic sigma weight residual 180.00 -153.29 -26.71 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA TYR A 266 " pdb=" C TYR A 266 " pdb=" N LEU A 267 " pdb=" CA LEU A 267 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 1566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 144 0.052 - 0.104: 109 0.104 - 0.156: 103 0.156 - 0.208: 40 0.208 - 0.259: 10 Chirality restraints: 406 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.92e+01 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 -2.55 0.15 2.00e-02 2.50e+03 5.41e+01 chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.53 -0.13 2.00e-02 2.50e+03 3.93e+01 ... (remaining 403 not shown) Planarity restraints: 400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 256 " 0.116 2.00e-02 2.50e+03 7.16e-02 1.02e+02 pdb=" CG TYR A 256 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 256 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 TYR A 256 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR A 256 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A 256 " -0.061 2.00e-02 2.50e+03 pdb=" CZ TYR A 256 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR A 256 " 0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 132 " -0.048 2.00e-02 2.50e+03 4.79e-02 2.86e+01 pdb=" CG ASN A 132 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 132 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 132 " 0.070 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 50 " 0.071 2.00e-02 2.50e+03 3.75e-02 2.82e+01 pdb=" CG TYR A 50 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 50 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A 50 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 50 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 50 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 50 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 50 " 0.054 2.00e-02 2.50e+03 ... (remaining 397 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 1396 3.05 - 3.51: 2140 3.51 - 3.97: 4151 3.97 - 4.44: 4576 4.44 - 4.90: 7431 Nonbonded interactions: 19694 Sorted by model distance: nonbonded pdb=" OD1 ASN A 108 " pdb=" OG SER A 119 " model vdw 2.582 3.040 nonbonded pdb=" OG SER A 36 " pdb=" O TYR A 38 " model vdw 2.585 3.040 nonbonded pdb=" OE2 GLU A 120 " pdb=" OG SER A 165 " model vdw 2.597 3.040 nonbonded pdb=" OD1 ASP A 17 " pdb=" O6 NAG C 1 " model vdw 2.604 3.040 nonbonded pdb=" OG1 THR A 154 " pdb=" OD1 ASP A 177 " model vdw 2.605 3.040 ... (remaining 19689 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 'D' } 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: 4.250 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 13.070 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9169 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 : 0.015 0.073 2445 Z= 0.806 Angle : 1.719 8.527 3356 Z= 1.073 Chirality : 0.103 0.259 406 Planarity : 0.015 0.133 393 Dihedral : 14.403 101.301 1052 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.40 % Allowed : 0.00 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.45), residues: 266 helix: None (None), residues: 0 sheet: 0.17 (0.49), residues: 85 loop : -1.13 (0.41), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.010 TRP A 89 HIS 0.009 0.005 HIS A 175 PHE 0.041 0.011 PHE A 18 TYR 0.125 0.019 TYR A 256 ARG 0.011 0.002 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.01098 ( 7) link_NAG-ASN : angle 4.45623 ( 21) link_ALPHA1-6 : bond 0.03112 ( 1) link_ALPHA1-6 : angle 4.32625 ( 3) link_BETA1-4 : bond 0.02177 ( 4) link_BETA1-4 : angle 4.09138 ( 12) link_ALPHA1-3 : bond 0.02740 ( 1) link_ALPHA1-3 : angle 5.14243 ( 3) hydrogen bonds : bond 0.09595 ( 69) hydrogen bonds : angle 7.89310 ( 177) SS BOND : bond 0.00429 ( 3) SS BOND : angle 1.40628 ( 6) covalent geometry : bond 0.01482 ( 2429) covalent geometry : angle 1.66289 ( 3311) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.283 Fit side-chains REVERT: A 54 ARG cc_start: 0.9093 (mtt180) cc_final: 0.7395 (mmm160) REVERT: A 92 LYS cc_start: 0.9113 (mtpt) cc_final: 0.8802 (mttp) REVERT: A 114 ASN cc_start: 0.8335 (m-40) cc_final: 0.8130 (m-40) REVERT: A 115 LYS cc_start: 0.8630 (mmmm) cc_final: 0.8325 (mmtm) REVERT: A 155 MET cc_start: 0.9363 (mmm) cc_final: 0.8970 (mmm) REVERT: A 163 CYS cc_start: 0.8620 (m) cc_final: 0.8291 (m) REVERT: A 187 LYS cc_start: 0.9152 (tttt) cc_final: 0.8826 (tttp) REVERT: A 221 THR cc_start: 0.9204 (m) cc_final: 0.8981 (p) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 1.5640 time to fit residues: 68.5498 Evaluate side-chains 25 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3060 r_free = 0.3060 target = 0.083003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.068627 restraints weight = 3138.562| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 1.92 r_work: 0.2722 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2445 Z= 0.186 Angle : 0.701 4.575 3356 Z= 0.361 Chirality : 0.047 0.208 406 Planarity : 0.004 0.028 393 Dihedral : 10.690 79.505 566 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.62 % Allowed : 3.24 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.48), residues: 266 helix: None (None), residues: 0 sheet: 0.50 (0.51), residues: 90 loop : -0.89 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 174 HIS 0.002 0.001 HIS A 175 PHE 0.019 0.002 PHE A 121 TYR 0.018 0.002 TYR A 90 ARG 0.001 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 7) link_NAG-ASN : angle 2.14254 ( 21) link_ALPHA1-6 : bond 0.00833 ( 1) link_ALPHA1-6 : angle 1.38310 ( 3) link_BETA1-4 : bond 0.00246 ( 4) link_BETA1-4 : angle 2.27155 ( 12) link_ALPHA1-3 : bond 0.00508 ( 1) link_ALPHA1-3 : angle 1.48428 ( 3) hydrogen bonds : bond 0.04882 ( 69) hydrogen bonds : angle 7.11729 ( 177) SS BOND : bond 0.00097 ( 3) SS BOND : angle 1.06401 ( 6) covalent geometry : bond 0.00429 ( 2429) covalent geometry : angle 0.66670 ( 3311) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.224 Fit side-chains REVERT: A 54 ARG cc_start: 0.9232 (mtt180) cc_final: 0.7330 (mmm-85) REVERT: A 115 LYS cc_start: 0.8678 (mmmm) cc_final: 0.8327 (mmtm) REVERT: A 247 SER cc_start: 0.8911 (p) cc_final: 0.8573 (m) outliers start: 4 outliers final: 0 residues processed: 29 average time/residue: 1.5480 time to fit residues: 45.8490 Evaluate side-chains 25 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.081092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.066995 restraints weight = 3138.426| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.87 r_work: 0.2703 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 2445 Z= 0.234 Angle : 0.704 4.568 3356 Z= 0.363 Chirality : 0.047 0.222 406 Planarity : 0.004 0.032 393 Dihedral : 10.253 75.483 566 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.81 % Allowed : 5.26 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.49), residues: 266 helix: None (None), residues: 0 sheet: 0.34 (0.51), residues: 96 loop : -0.86 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 174 HIS 0.002 0.001 HIS A 160 PHE 0.019 0.002 PHE A 121 TYR 0.018 0.002 TYR A 66 ARG 0.002 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 7) link_NAG-ASN : angle 2.02618 ( 21) link_ALPHA1-6 : bond 0.01050 ( 1) link_ALPHA1-6 : angle 1.20347 ( 3) link_BETA1-4 : bond 0.00254 ( 4) link_BETA1-4 : angle 2.12416 ( 12) link_ALPHA1-3 : bond 0.00752 ( 1) link_ALPHA1-3 : angle 1.21264 ( 3) hydrogen bonds : bond 0.04570 ( 69) hydrogen bonds : angle 7.10160 ( 177) SS BOND : bond 0.00171 ( 3) SS BOND : angle 1.81444 ( 6) covalent geometry : bond 0.00536 ( 2429) covalent geometry : angle 0.67208 ( 3311) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.278 Fit side-chains REVERT: A 54 ARG cc_start: 0.9225 (mtt180) cc_final: 0.7311 (mmm-85) REVERT: A 115 LYS cc_start: 0.8709 (mmmm) cc_final: 0.8332 (mmtm) REVERT: A 247 SER cc_start: 0.8897 (p) cc_final: 0.8601 (m) outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 1.7488 time to fit residues: 44.6540 Evaluate side-chains 24 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3044 r_free = 0.3044 target = 0.081898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.067946 restraints weight = 3137.096| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.87 r_work: 0.2719 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9155 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2445 Z= 0.200 Angle : 0.671 5.809 3356 Z= 0.344 Chirality : 0.046 0.231 406 Planarity : 0.004 0.036 393 Dihedral : 9.847 72.175 566 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.81 % Allowed : 6.48 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.50), residues: 266 helix: None (None), residues: 0 sheet: 0.29 (0.52), residues: 95 loop : -0.90 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 174 HIS 0.001 0.001 HIS A 234 PHE 0.016 0.002 PHE A 121 TYR 0.015 0.002 TYR A 66 ARG 0.002 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 7) link_NAG-ASN : angle 1.87586 ( 21) link_ALPHA1-6 : bond 0.01141 ( 1) link_ALPHA1-6 : angle 1.10850 ( 3) link_BETA1-4 : bond 0.00193 ( 4) link_BETA1-4 : angle 1.96423 ( 12) link_ALPHA1-3 : bond 0.00697 ( 1) link_ALPHA1-3 : angle 1.26464 ( 3) hydrogen bonds : bond 0.04250 ( 69) hydrogen bonds : angle 7.05224 ( 177) SS BOND : bond 0.00131 ( 3) SS BOND : angle 2.41696 ( 6) covalent geometry : bond 0.00450 ( 2429) covalent geometry : angle 0.63755 ( 3311) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.259 Fit side-chains REVERT: A 54 ARG cc_start: 0.9217 (mtt180) cc_final: 0.7318 (mmm-85) REVERT: A 115 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8312 (mmtm) REVERT: A 247 SER cc_start: 0.8904 (p) cc_final: 0.8590 (m) outliers start: 2 outliers final: 1 residues processed: 26 average time/residue: 1.9343 time to fit residues: 51.2313 Evaluate side-chains 27 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 5 optimal weight: 0.4980 chunk 3 optimal weight: 0.3980 chunk 12 optimal weight: 0.0050 chunk 10 optimal weight: 0.5980 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 = 0.3082 r_free = 0.3082 target = 0.084203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.069783 restraints weight = 3187.239| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.94 r_work: 0.2746 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2445 Z= 0.150 Angle : 0.617 5.380 3356 Z= 0.318 Chirality : 0.044 0.238 406 Planarity : 0.004 0.038 393 Dihedral : 9.286 67.085 566 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.21 % Allowed : 5.67 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.50), residues: 266 helix: None (None), residues: 0 sheet: 0.10 (0.55), residues: 86 loop : -0.80 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 174 HIS 0.002 0.000 HIS A 201 PHE 0.015 0.002 PHE A 121 TYR 0.013 0.001 TYR A 66 ARG 0.002 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 7) link_NAG-ASN : angle 1.70759 ( 21) link_ALPHA1-6 : bond 0.01272 ( 1) link_ALPHA1-6 : angle 1.02073 ( 3) link_BETA1-4 : bond 0.00193 ( 4) link_BETA1-4 : angle 1.73940 ( 12) link_ALPHA1-3 : bond 0.00795 ( 1) link_ALPHA1-3 : angle 1.39742 ( 3) hydrogen bonds : bond 0.03920 ( 69) hydrogen bonds : angle 6.98043 ( 177) SS BOND : bond 0.00624 ( 3) SS BOND : angle 2.58268 ( 6) covalent geometry : bond 0.00332 ( 2429) covalent geometry : angle 0.58425 ( 3311) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.399 Fit side-chains REVERT: A 54 ARG cc_start: 0.9229 (mtt180) cc_final: 0.7312 (mmm-85) REVERT: A 115 LYS cc_start: 0.8700 (mmmm) cc_final: 0.8308 (mmtm) REVERT: A 247 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8583 (m) outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 1.9738 time to fit residues: 54.2710 Evaluate side-chains 28 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 247 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.0870 chunk 11 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3071 r_free = 0.3071 target = 0.083412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.069087 restraints weight = 3133.645| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 1.91 r_work: 0.2736 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2445 Z= 0.169 Angle : 0.620 5.002 3356 Z= 0.318 Chirality : 0.045 0.251 406 Planarity : 0.004 0.039 393 Dihedral : 9.079 65.101 566 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.21 % Allowed : 6.88 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.13 (0.56), residues: 86 loop : -0.74 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 PHE 0.015 0.002 PHE A 121 TYR 0.014 0.002 TYR A 66 ARG 0.002 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 7) link_NAG-ASN : angle 1.70430 ( 21) link_ALPHA1-6 : bond 0.01292 ( 1) link_ALPHA1-6 : angle 1.00861 ( 3) link_BETA1-4 : bond 0.00188 ( 4) link_BETA1-4 : angle 1.77996 ( 12) link_ALPHA1-3 : bond 0.00761 ( 1) link_ALPHA1-3 : angle 1.39565 ( 3) hydrogen bonds : bond 0.03924 ( 69) hydrogen bonds : angle 7.01279 ( 177) SS BOND : bond 0.00387 ( 3) SS BOND : angle 2.44726 ( 6) covalent geometry : bond 0.00378 ( 2429) covalent geometry : angle 0.58800 ( 3311) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.269 Fit side-chains REVERT: A 54 ARG cc_start: 0.9227 (mtt180) cc_final: 0.7308 (mmm-85) REVERT: A 115 LYS cc_start: 0.8680 (mmmm) cc_final: 0.8270 (mmtm) REVERT: A 247 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8577 (m) outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 1.9798 time to fit residues: 52.4688 Evaluate side-chains 28 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 247 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3049 r_free = 0.3049 target = 0.082070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.067785 restraints weight = 3175.280| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.92 r_work: 0.2712 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9147 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2445 Z= 0.214 Angle : 0.654 5.003 3356 Z= 0.335 Chirality : 0.046 0.258 406 Planarity : 0.004 0.039 393 Dihedral : 9.215 65.781 566 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.21 % Allowed : 7.69 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.50), residues: 266 helix: None (None), residues: 0 sheet: 0.09 (0.56), residues: 86 loop : -0.77 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 PHE 0.016 0.002 PHE A 18 TYR 0.015 0.002 TYR A 66 ARG 0.002 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 7) link_NAG-ASN : angle 1.78210 ( 21) link_ALPHA1-6 : bond 0.01225 ( 1) link_ALPHA1-6 : angle 0.98569 ( 3) link_BETA1-4 : bond 0.00198 ( 4) link_BETA1-4 : angle 1.89635 ( 12) link_ALPHA1-3 : bond 0.00681 ( 1) link_ALPHA1-3 : angle 1.33709 ( 3) hydrogen bonds : bond 0.04072 ( 69) hydrogen bonds : angle 7.13732 ( 177) SS BOND : bond 0.00427 ( 3) SS BOND : angle 2.55815 ( 6) covalent geometry : bond 0.00481 ( 2429) covalent geometry : angle 0.62083 ( 3311) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.249 Fit side-chains REVERT: A 54 ARG cc_start: 0.9227 (mtt180) cc_final: 0.7298 (mmm-85) REVERT: A 213 TYR cc_start: 0.9205 (OUTLIER) cc_final: 0.8785 (p90) REVERT: A 247 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8551 (m) outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 1.9062 time to fit residues: 50.4484 Evaluate side-chains 29 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 247 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 19 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3060 r_free = 0.3060 target = 0.082699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.068403 restraints weight = 3217.386| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.93 r_work: 0.2722 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2445 Z= 0.185 Angle : 0.628 4.851 3356 Z= 0.323 Chirality : 0.045 0.256 406 Planarity : 0.004 0.040 393 Dihedral : 9.038 64.025 566 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.21 % Allowed : 8.10 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.09 (0.56), residues: 86 loop : -0.79 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 174 HIS 0.001 0.000 HIS A 234 PHE 0.014 0.002 PHE A 121 TYR 0.014 0.002 TYR A 66 ARG 0.003 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 7) link_NAG-ASN : angle 1.72175 ( 21) link_ALPHA1-6 : bond 0.01249 ( 1) link_ALPHA1-6 : angle 0.98739 ( 3) link_BETA1-4 : bond 0.00187 ( 4) link_BETA1-4 : angle 1.78257 ( 12) link_ALPHA1-3 : bond 0.00701 ( 1) link_ALPHA1-3 : angle 1.39557 ( 3) hydrogen bonds : bond 0.03936 ( 69) hydrogen bonds : angle 7.10987 ( 177) SS BOND : bond 0.00399 ( 3) SS BOND : angle 2.32523 ( 6) covalent geometry : bond 0.00413 ( 2429) covalent geometry : angle 0.59794 ( 3311) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.273 Fit side-chains REVERT: A 54 ARG cc_start: 0.9225 (mtt180) cc_final: 0.7294 (mmm-85) REVERT: A 213 TYR cc_start: 0.9216 (OUTLIER) cc_final: 0.8810 (p90) REVERT: A 247 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8614 (m) outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 1.8606 time to fit residues: 51.1889 Evaluate side-chains 29 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 247 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3065 r_free = 0.3065 target = 0.082583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.068245 restraints weight = 3100.431| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.91 r_work: 0.2734 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 2445 Z= 0.209 Angle : 0.649 4.902 3356 Z= 0.334 Chirality : 0.046 0.261 406 Planarity : 0.004 0.040 393 Dihedral : 9.068 63.881 566 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.21 % Allowed : 8.50 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.50), residues: 266 helix: None (None), residues: 0 sheet: 0.07 (0.56), residues: 86 loop : -0.79 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 PHE 0.015 0.002 PHE A 18 TYR 0.014 0.002 TYR A 66 ARG 0.003 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 7) link_NAG-ASN : angle 1.76476 ( 21) link_ALPHA1-6 : bond 0.01223 ( 1) link_ALPHA1-6 : angle 0.99306 ( 3) link_BETA1-4 : bond 0.00187 ( 4) link_BETA1-4 : angle 1.83695 ( 12) link_ALPHA1-3 : bond 0.00667 ( 1) link_ALPHA1-3 : angle 1.35277 ( 3) hydrogen bonds : bond 0.04034 ( 69) hydrogen bonds : angle 7.15201 ( 177) SS BOND : bond 0.00532 ( 3) SS BOND : angle 2.60068 ( 6) covalent geometry : bond 0.00476 ( 2429) covalent geometry : angle 0.61655 ( 3311) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.305 Fit side-chains REVERT: A 54 ARG cc_start: 0.9241 (mtt180) cc_final: 0.7364 (mmm-85) REVERT: A 213 TYR cc_start: 0.9251 (OUTLIER) cc_final: 0.8852 (p90) REVERT: A 247 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8658 (m) outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 1.9354 time to fit residues: 51.2714 Evaluate side-chains 29 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 247 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3070 r_free = 0.3070 target = 0.082849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.068555 restraints weight = 3150.146| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 1.91 r_work: 0.2738 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9167 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2445 Z= 0.194 Angle : 0.636 4.885 3356 Z= 0.327 Chirality : 0.046 0.261 406 Planarity : 0.004 0.040 393 Dihedral : 8.922 62.262 566 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.21 % Allowed : 8.50 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.08 (0.56), residues: 86 loop : -0.80 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 174 HIS 0.001 0.001 HIS A 201 PHE 0.014 0.002 PHE A 121 TYR 0.014 0.002 TYR A 66 ARG 0.003 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 7) link_NAG-ASN : angle 1.73502 ( 21) link_ALPHA1-6 : bond 0.01238 ( 1) link_ALPHA1-6 : angle 0.99113 ( 3) link_BETA1-4 : bond 0.00184 ( 4) link_BETA1-4 : angle 1.77789 ( 12) link_ALPHA1-3 : bond 0.00660 ( 1) link_ALPHA1-3 : angle 1.38967 ( 3) hydrogen bonds : bond 0.03960 ( 69) hydrogen bonds : angle 7.15439 ( 177) SS BOND : bond 0.00515 ( 3) SS BOND : angle 2.40634 ( 6) covalent geometry : bond 0.00439 ( 2429) covalent geometry : angle 0.60477 ( 3311) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 532 Ramachandran restraints generated. 266 Oldfield, 0 Emsley, 266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.278 Fit side-chains REVERT: A 54 ARG cc_start: 0.9236 (mtt180) cc_final: 0.7360 (mmm-85) REVERT: A 213 TYR cc_start: 0.9268 (OUTLIER) cc_final: 0.8799 (p90) REVERT: A 247 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8661 (m) outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 1.9289 time to fit residues: 51.0783 Evaluate side-chains 29 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 247 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.0270 chunk 9 optimal weight: 0.8980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 = 0.3084 r_free = 0.3084 target = 0.083711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.069433 restraints weight = 3150.801| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.93 r_work: 0.2754 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9155 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2445 Z= 0.162 Angle : 0.606 4.806 3356 Z= 0.313 Chirality : 0.045 0.260 406 Planarity : 0.004 0.040 393 Dihedral : 8.635 59.464 566 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.21 % Allowed : 8.50 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.10 (0.56), residues: 86 loop : -0.80 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 174 HIS 0.001 0.000 HIS A 201 PHE 0.014 0.002 PHE A 121 TYR 0.013 0.001 TYR A 66 ARG 0.003 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 7) link_NAG-ASN : angle 1.66182 ( 21) link_ALPHA1-6 : bond 0.01291 ( 1) link_ALPHA1-6 : angle 0.99278 ( 3) link_BETA1-4 : bond 0.00188 ( 4) link_BETA1-4 : angle 1.66105 ( 12) link_ALPHA1-3 : bond 0.00720 ( 1) link_ALPHA1-3 : angle 1.46654 ( 3) hydrogen bonds : bond 0.03815 ( 69) hydrogen bonds : angle 7.07696 ( 177) SS BOND : bond 0.00436 ( 3) SS BOND : angle 2.11068 ( 6) covalent geometry : bond 0.00364 ( 2429) covalent geometry : angle 0.57759 ( 3311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2916.27 seconds wall clock time: 50 minutes 48.14 seconds (3048.14 seconds total)