Starting phenix.real_space_refine on Wed Sep 17 05:01:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n17_48808/09_2025/9n17_48808_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n17_48808/09_2025/9n17_48808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n17_48808/09_2025/9n17_48808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n17_48808/09_2025/9n17_48808.map" model { file = "/net/cci-nas-00/data/ceres_data/9n17_48808/09_2025/9n17_48808_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n17_48808/09_2025/9n17_48808_trim.cif" } resolution = 3.09 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= 0.001 sd= 0.038 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: 5 Type Number sf(0) Gaussians S 9 5.16 5 C 1521 2.51 5 N 353 2.21 5 O 476 1.98 5 H 2095 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s 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: 4454 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 4281 Classifications: {'peptide': 268} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 259} Chain: "B" 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: "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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.38, per 1000 atoms: 0.31 Number of scatterers: 4454 At special positions: 0 Unit cell: (68.1035, 58.8691, 77.3379, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 476 8.00 N 353 7.00 C 1521 6.00 H 2095 1.00 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 B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A1401 " - " ASN A 19 " " NAG A1402 " - " ASN A 58 " " NAG A1403 " - " ASN A 171 " " NAG A1404 " - " ASN A 192 " " NAG A1405 " - " ASN A 251 " " NAG A1406 " - " ASN A 29 " " NAG B 1 " - " ASN A 132 " " NAG C 1 " - " ASN A 188 " Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 112.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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, 45.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.793A 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 36 through 39 removed outlier: 4.348A pdb=" N SER A 36 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN A 73 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY A 101 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 68 removed outlier: 3.730A 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: 8.187A pdb=" N THR A 241 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 7.318A 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: 3.524A 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 73 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: 0.89 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 2094 1.13 - 1.30: 348 1.30 - 1.47: 997 1.47 - 1.64: 1067 1.64 - 1.81: 11 Bond restraints: 4517 Sorted by residual: bond pdb=" N TYR A 227 " pdb=" H TYR A 227 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N ASN A 132 " pdb=" H ASN A 132 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" CE1 TYR A 212 " pdb=" HE1 TYR A 212 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N LYS A 186 " pdb=" H LYS A 186 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N THR A 154 " pdb=" H THR A 154 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 4512 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 6802 2.47 - 4.94: 958 4.94 - 7.41: 248 7.41 - 9.89: 5 9.89 - 12.36: 1 Bond angle restraints: 8014 Sorted by residual: angle pdb=" CA ILE A 15 " pdb=" C ILE A 15 " pdb=" N GLY A 16 " ideal model delta sigma weight residual 115.45 121.78 -6.33 1.18e+00 7.18e-01 2.87e+01 angle pdb=" CB HIS A 234 " pdb=" CG HIS A 234 " pdb=" CD2 HIS A 234 " ideal model delta sigma weight residual 131.20 124.80 6.40 1.30e+00 5.92e-01 2.43e+01 angle pdb=" CB HIS A 201 " pdb=" CG HIS A 201 " pdb=" CD2 HIS A 201 " ideal model delta sigma weight residual 131.20 125.32 5.88 1.30e+00 5.92e-01 2.04e+01 angle pdb=" N ILE A 15 " pdb=" CA ILE A 15 " pdb=" C ILE A 15 " ideal model delta sigma weight residual 110.05 105.43 4.62 1.09e+00 8.42e-01 1.80e+01 angle pdb=" CA PHE A 121 " pdb=" CB PHE A 121 " pdb=" CG PHE A 121 " ideal model delta sigma weight residual 113.80 117.92 -4.12 1.00e+00 1.00e+00 1.70e+01 ... (remaining 8009 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 20.17: 2211 20.17 - 40.33: 86 40.33 - 60.49: 43 60.49 - 80.65: 16 80.65 - 100.81: 5 Dihedral angle restraints: 2361 sinusoidal: 1332 harmonic: 1029 Sorted by residual: dihedral pdb=" CA ASN A 73 " pdb=" C ASN A 73 " pdb=" N PHE A 74 " pdb=" CA PHE A 74 " ideal model delta harmonic sigma weight residual 180.00 151.83 28.17 0 5.00e+00 4.00e-02 3.17e+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 180.00 153.30 26.70 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA VAL A 14 " pdb=" C VAL A 14 " pdb=" N ILE A 15 " pdb=" CA ILE A 15 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 2358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 170 0.067 - 0.134: 155 0.134 - 0.201: 73 0.201 - 0.268: 6 0.268 - 0.335: 2 Chirality restraints: 406 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.81e+01 chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.35e+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 -2.52 0.12 2.00e-02 2.50e+03 3.64e+01 ... (remaining 403 not shown) Planarity restraints: 658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 29 " 0.175 2.00e-02 2.50e+03 1.33e-01 2.67e+02 pdb=" CG ASN A 29 " -0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN A 29 " -0.073 2.00e-02 2.50e+03 pdb=" ND2 ASN A 29 " -0.138 2.00e-02 2.50e+03 pdb="HD21 ASN A 29 " -0.094 2.00e-02 2.50e+03 pdb=" C1 NAG A1406 " 0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 132 " -0.094 2.00e-02 2.50e+03 7.44e-02 8.30e+01 pdb=" CG ASN A 132 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 132 " 0.037 2.00e-02 2.50e+03 pdb=" ND2 ASN A 132 " 0.091 2.00e-02 2.50e+03 pdb="HD21 ASN A 132 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 206 " 0.461 9.50e-02 1.11e+02 1.61e-01 7.92e+01 pdb=" NE ARG A 206 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 206 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 206 " -0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG A 206 " -0.056 2.00e-02 2.50e+03 pdb="HH11 ARG A 206 " -0.051 2.00e-02 2.50e+03 pdb="HH12 ARG A 206 " 0.045 2.00e-02 2.50e+03 pdb="HH21 ARG A 206 " -0.046 2.00e-02 2.50e+03 pdb="HH22 ARG A 206 " 0.080 2.00e-02 2.50e+03 ... (remaining 655 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 344 2.21 - 2.81: 7936 2.81 - 3.41: 11571 3.41 - 4.00: 16631 4.00 - 4.60: 23938 Nonbonded interactions: 60420 Sorted by model distance: nonbonded pdb=" HH TYR A 66 " pdb=" OE1 GLU A 205 " model vdw 1.614 2.450 nonbonded pdb=" OE2 GLU A 120 " pdb=" HG SER A 165 " model vdw 1.616 2.450 nonbonded pdb=" HG1 THR A 154 " pdb=" OD1 ASP A 177 " model vdw 1.621 2.450 nonbonded pdb=" OD1 ASN A 108 " pdb=" HG SER A 119 " model vdw 1.650 2.450 nonbonded pdb=" OD1 ASP A 41 " pdb=" HG SER A 43 " model vdw 1.653 2.450 ... (remaining 60415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 0.040 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.070 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 0.076 2438 Z= 0.805 Angle : 1.663 8.775 3346 Z= 1.043 Chirality : 0.103 0.335 406 Planarity : 0.013 0.138 391 Dihedral : 14.202 100.807 1046 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 0.22 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.27 % Favored : 91.35 % Rotamer: Outliers : 0.40 % Allowed : 0.00 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.34 (0.45), residues: 266 helix: None (None), residues: 0 sheet: 0.33 (0.48), residues: 89 loop : -1.66 (0.41), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 206 TYR 0.084 0.014 TYR A 256 PHE 0.077 0.012 PHE A 74 TRP 0.052 0.013 TRP A 197 HIS 0.007 0.004 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.01485 ( 2422) covalent geometry : angle 1.61710 ( 3301) SS BOND : bond 0.00613 ( 3) SS BOND : angle 2.09259 ( 6) hydrogen bonds : bond 0.11845 ( 73) hydrogen bonds : angle 8.05026 ( 192) link_ALPHA1-3 : bond 0.02323 ( 1) link_ALPHA1-3 : angle 2.52347 ( 3) link_ALPHA1-6 : bond 0.02388 ( 1) link_ALPHA1-6 : angle 2.63557 ( 3) link_BETA1-4 : bond 0.02215 ( 3) link_BETA1-4 : angle 3.58620 ( 9) link_NAG-ASN : bond 0.00915 ( 8) link_NAG-ASN : angle 4.27323 ( 24) *********************** 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 46 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8358 (mt-10) REVERT: A 54 ARG cc_start: 0.8887 (mtt180) cc_final: 0.7927 (mtt-85) REVERT: A 90 TYR cc_start: 0.9303 (m-80) cc_final: 0.9067 (m-80) REVERT: A 104 SER cc_start: 0.9756 (m) cc_final: 0.9224 (p) REVERT: A 163 CYS cc_start: 0.7470 (m) cc_final: 0.7099 (m) REVERT: A 206 ARG cc_start: 0.8945 (mtm-85) cc_final: 0.7748 (tpt170) REVERT: A 216 SER cc_start: 0.9450 (t) cc_final: 0.9245 (p) outliers start: 1 outliers final: 1 residues processed: 45 average time/residue: 0.3015 time to fit residues: 14.6213 Evaluate side-chains 30 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3080 r_free = 0.3080 target = 0.072992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.055367 restraints weight = 14226.056| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.40 r_work: 0.2610 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 2438 Z= 0.180 Angle : 0.812 11.578 3346 Z= 0.420 Chirality : 0.048 0.325 406 Planarity : 0.004 0.031 391 Dihedral : 11.748 77.572 567 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.40 % Allowed : 4.45 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.94 (0.47), residues: 266 helix: None (None), residues: 0 sheet: 0.55 (0.50), residues: 96 loop : -1.42 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 264 TYR 0.020 0.001 TYR A 38 PHE 0.015 0.002 PHE A 74 TRP 0.010 0.001 TRP A 174 HIS 0.002 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 2422) covalent geometry : angle 0.76300 ( 3301) SS BOND : bond 0.00822 ( 3) SS BOND : angle 3.45497 ( 6) hydrogen bonds : bond 0.04254 ( 73) hydrogen bonds : angle 7.18473 ( 192) link_ALPHA1-3 : bond 0.00899 ( 1) link_ALPHA1-3 : angle 2.39033 ( 3) link_ALPHA1-6 : bond 0.00783 ( 1) link_ALPHA1-6 : angle 2.35217 ( 3) link_BETA1-4 : bond 0.00247 ( 3) link_BETA1-4 : angle 2.03412 ( 9) link_NAG-ASN : bond 0.00275 ( 8) link_NAG-ASN : angle 2.42008 ( 24) *********************** 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 31 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8306 (mt-10) REVERT: A 54 ARG cc_start: 0.8842 (mtt180) cc_final: 0.7395 (mmm160) REVERT: A 104 SER cc_start: 0.9676 (m) cc_final: 0.9354 (p) REVERT: A 120 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8277 (mm-30) REVERT: A 163 CYS cc_start: 0.7028 (m) cc_final: 0.6665 (m) REVERT: A 206 ARG cc_start: 0.9021 (mtm-85) cc_final: 0.8071 (tpt170) REVERT: A 216 SER cc_start: 0.9374 (t) cc_final: 0.9166 (p) outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 0.2085 time to fit residues: 7.0677 Evaluate side-chains 25 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- 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 = 0.3026 r_free = 0.3026 target = 0.070728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.053218 restraints weight = 14191.473| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 3.36 r_work: 0.2545 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 2438 Z= 0.205 Angle : 0.687 8.687 3346 Z= 0.356 Chirality : 0.045 0.210 406 Planarity : 0.004 0.035 391 Dihedral : 10.726 68.949 567 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.40 % Allowed : 7.69 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.91 (0.48), residues: 266 helix: None (None), residues: 0 sheet: 0.32 (0.51), residues: 93 loop : -1.19 (0.45), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.016 0.001 TYR A 38 PHE 0.019 0.002 PHE A 74 TRP 0.006 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 2422) covalent geometry : angle 0.65003 ( 3301) SS BOND : bond 0.00997 ( 3) SS BOND : angle 3.49921 ( 6) hydrogen bonds : bond 0.03793 ( 73) hydrogen bonds : angle 6.60929 ( 192) link_ALPHA1-3 : bond 0.01220 ( 1) link_ALPHA1-3 : angle 1.60887 ( 3) link_ALPHA1-6 : bond 0.00538 ( 1) link_ALPHA1-6 : angle 2.00883 ( 3) link_BETA1-4 : bond 0.00164 ( 3) link_BETA1-4 : angle 1.36914 ( 9) link_NAG-ASN : bond 0.00314 ( 8) link_NAG-ASN : angle 1.76185 ( 24) *********************** 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: 1 poor density : 26 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8323 (mt-10) REVERT: A 54 ARG cc_start: 0.8926 (mtt180) cc_final: 0.7521 (mtp85) REVERT: A 163 CYS cc_start: 0.6954 (m) cc_final: 0.6671 (m) REVERT: A 206 ARG cc_start: 0.9174 (mtm-85) cc_final: 0.8102 (tpt170) REVERT: A 216 SER cc_start: 0.9375 (t) cc_final: 0.9171 (p) outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.2158 time to fit residues: 6.3218 Evaluate side-chains 25 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3043 r_free = 0.3043 target = 0.071686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.054085 restraints weight = 14264.356| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 3.42 r_work: 0.2543 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 2438 Z= 0.144 Angle : 0.614 5.803 3346 Z= 0.316 Chirality : 0.044 0.226 406 Planarity : 0.004 0.034 391 Dihedral : 9.715 60.213 567 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.81 % Allowed : 6.88 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.99 (0.49), residues: 266 helix: None (None), residues: 0 sheet: 0.14 (0.50), residues: 93 loop : -1.16 (0.45), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 273 TYR 0.013 0.001 TYR A 38 PHE 0.015 0.001 PHE A 74 TRP 0.006 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2422) covalent geometry : angle 0.57578 ( 3301) SS BOND : bond 0.00991 ( 3) SS BOND : angle 3.31679 ( 6) hydrogen bonds : bond 0.03365 ( 73) hydrogen bonds : angle 6.30012 ( 192) link_ALPHA1-3 : bond 0.01136 ( 1) link_ALPHA1-3 : angle 1.77128 ( 3) link_ALPHA1-6 : bond 0.00768 ( 1) link_ALPHA1-6 : angle 2.08849 ( 3) link_BETA1-4 : bond 0.00145 ( 3) link_BETA1-4 : angle 1.31686 ( 9) link_NAG-ASN : bond 0.00142 ( 8) link_NAG-ASN : angle 1.61509 ( 24) *********************** 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 : 0.130 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8424 (mt-10) REVERT: A 54 ARG cc_start: 0.8963 (mtt180) cc_final: 0.7702 (mtp85) REVERT: A 61 ILE cc_start: 0.8952 (mm) cc_final: 0.8679 (mm) REVERT: A 163 CYS cc_start: 0.7006 (m) cc_final: 0.6471 (m) REVERT: A 206 ARG cc_start: 0.9240 (mtm-85) cc_final: 0.7942 (tpp-160) REVERT: A 216 SER cc_start: 0.9426 (t) cc_final: 0.9206 (p) outliers start: 2 outliers final: 1 residues processed: 26 average time/residue: 0.2075 time to fit residues: 6.1283 Evaluate side-chains 25 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 20 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3066 r_free = 0.3066 target = 0.072814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.056326 restraints weight = 14443.447| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 3.27 r_work: 0.2535 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2438 Z= 0.131 Angle : 0.574 5.770 3346 Z= 0.291 Chirality : 0.043 0.238 406 Planarity : 0.004 0.036 391 Dihedral : 8.797 51.972 567 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.21 % Allowed : 7.29 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.94 (0.49), residues: 266 helix: None (None), residues: 0 sheet: 0.16 (0.50), residues: 93 loop : -1.11 (0.47), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 273 TYR 0.012 0.001 TYR A 212 PHE 0.015 0.001 PHE A 74 TRP 0.005 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 2422) covalent geometry : angle 0.54818 ( 3301) SS BOND : bond 0.00423 ( 3) SS BOND : angle 2.07046 ( 6) hydrogen bonds : bond 0.03153 ( 73) hydrogen bonds : angle 6.03580 ( 192) link_ALPHA1-3 : bond 0.00986 ( 1) link_ALPHA1-3 : angle 1.58190 ( 3) link_ALPHA1-6 : bond 0.00888 ( 1) link_ALPHA1-6 : angle 2.01546 ( 3) link_BETA1-4 : bond 0.00201 ( 3) link_BETA1-4 : angle 1.30382 ( 9) link_NAG-ASN : bond 0.00157 ( 8) link_NAG-ASN : angle 1.45178 ( 24) *********************** 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 29 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8414 (mt-10) REVERT: A 54 ARG cc_start: 0.8987 (mtt180) cc_final: 0.7736 (mtp85) REVERT: A 61 ILE cc_start: 0.8845 (mm) cc_final: 0.8570 (mm) REVERT: A 163 CYS cc_start: 0.6871 (m) cc_final: 0.6575 (m) REVERT: A 206 ARG cc_start: 0.9174 (mtm-85) cc_final: 0.8090 (tpt170) REVERT: A 216 SER cc_start: 0.9407 (t) cc_final: 0.9192 (p) outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.1597 time to fit residues: 4.8344 Evaluate side-chains 28 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3067 r_free = 0.3067 target = 0.073203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.055798 restraints weight = 14592.170| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 3.43 r_work: 0.2541 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2438 Z= 0.129 Angle : 0.559 4.266 3346 Z= 0.286 Chirality : 0.043 0.239 406 Planarity : 0.003 0.032 391 Dihedral : 8.094 49.724 567 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.62 % Allowed : 7.29 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.86 (0.50), residues: 266 helix: None (None), residues: 0 sheet: 0.20 (0.50), residues: 93 loop : -1.04 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 273 TYR 0.011 0.001 TYR A 212 PHE 0.013 0.001 PHE A 74 TRP 0.009 0.001 TRP A 174 HIS 0.002 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 2422) covalent geometry : angle 0.52769 ( 3301) SS BOND : bond 0.01612 ( 3) SS BOND : angle 2.72152 ( 6) hydrogen bonds : bond 0.03011 ( 73) hydrogen bonds : angle 5.72846 ( 192) link_ALPHA1-3 : bond 0.01088 ( 1) link_ALPHA1-3 : angle 1.70342 ( 3) link_ALPHA1-6 : bond 0.00901 ( 1) link_ALPHA1-6 : angle 1.92884 ( 3) link_BETA1-4 : bond 0.00074 ( 3) link_BETA1-4 : angle 1.26383 ( 9) link_NAG-ASN : bond 0.00140 ( 8) link_NAG-ASN : angle 1.42501 ( 24) *********************** 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 28 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 54 ARG cc_start: 0.8980 (mtt180) cc_final: 0.7786 (mtp85) REVERT: A 61 ILE cc_start: 0.8907 (mm) cc_final: 0.8634 (mm) REVERT: A 156 CYS cc_start: 0.8149 (m) cc_final: 0.7889 (m) REVERT: A 163 CYS cc_start: 0.6845 (m) cc_final: 0.6488 (m) REVERT: A 206 ARG cc_start: 0.9194 (mtm-85) cc_final: 0.8062 (tpm170) REVERT: A 216 SER cc_start: 0.9399 (t) cc_final: 0.9175 (p) outliers start: 4 outliers final: 4 residues processed: 25 average time/residue: 0.1570 time to fit residues: 4.5549 Evaluate side-chains 28 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.0570 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.2102 ------------------------------------------------------------------------------- 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 = 0.3056 r_free = 0.3056 target = 0.072709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.056125 restraints weight = 14498.836| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 3.29 r_work: 0.2538 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2438 Z= 0.164 Angle : 0.555 4.257 3346 Z= 0.283 Chirality : 0.043 0.235 406 Planarity : 0.003 0.032 391 Dihedral : 7.532 49.891 567 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.62 % Allowed : 6.48 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.90 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.10 (0.50), residues: 93 loop : -1.03 (0.49), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.010 0.001 TYR A 38 PHE 0.013 0.001 PHE A 74 TRP 0.007 0.001 TRP A 174 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 2422) covalent geometry : angle 0.52564 ( 3301) SS BOND : bond 0.01388 ( 3) SS BOND : angle 2.50654 ( 6) hydrogen bonds : bond 0.03150 ( 73) hydrogen bonds : angle 5.67125 ( 192) link_ALPHA1-3 : bond 0.00934 ( 1) link_ALPHA1-3 : angle 1.60072 ( 3) link_ALPHA1-6 : bond 0.01004 ( 1) link_ALPHA1-6 : angle 1.85943 ( 3) link_BETA1-4 : bond 0.00138 ( 3) link_BETA1-4 : angle 1.37223 ( 9) link_NAG-ASN : bond 0.00231 ( 8) link_NAG-ASN : angle 1.40985 ( 24) *********************** 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 30 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.9007 (mtt180) cc_final: 0.7791 (mtp85) REVERT: A 61 ILE cc_start: 0.8887 (mm) cc_final: 0.8604 (mm) REVERT: A 163 CYS cc_start: 0.6934 (m) cc_final: 0.6555 (m) REVERT: A 206 ARG cc_start: 0.9192 (mtm-85) cc_final: 0.8073 (tpm170) REVERT: A 216 SER cc_start: 0.9427 (t) cc_final: 0.9208 (p) REVERT: A 252 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8744 (mm-30) outliers start: 4 outliers final: 4 residues processed: 26 average time/residue: 0.1630 time to fit residues: 4.9457 Evaluate side-chains 29 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.073063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.056815 restraints weight = 14569.125| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 3.27 r_work: 0.2551 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2438 Z= 0.149 Angle : 0.535 3.863 3346 Z= 0.274 Chirality : 0.043 0.220 406 Planarity : 0.003 0.032 391 Dihedral : 7.192 51.090 567 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.21 % Allowed : 6.88 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.86 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.13 (0.51), residues: 93 loop : -1.01 (0.49), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 206 TYR 0.010 0.001 TYR A 212 PHE 0.013 0.001 PHE A 74 TRP 0.006 0.001 TRP A 174 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 2422) covalent geometry : angle 0.50544 ( 3301) SS BOND : bond 0.00976 ( 3) SS BOND : angle 2.47410 ( 6) hydrogen bonds : bond 0.03033 ( 73) hydrogen bonds : angle 5.55842 ( 192) link_ALPHA1-3 : bond 0.00846 ( 1) link_ALPHA1-3 : angle 1.51703 ( 3) link_ALPHA1-6 : bond 0.00953 ( 1) link_ALPHA1-6 : angle 1.88244 ( 3) link_BETA1-4 : bond 0.00154 ( 3) link_BETA1-4 : angle 1.36899 ( 9) link_NAG-ASN : bond 0.00171 ( 8) link_NAG-ASN : angle 1.31605 ( 24) *********************** 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 : 0.119 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9057 (p0) cc_final: 0.8839 (p0) REVERT: A 54 ARG cc_start: 0.9002 (mtt180) cc_final: 0.7814 (mtp85) REVERT: A 61 ILE cc_start: 0.8915 (mm) cc_final: 0.8638 (mm) REVERT: A 163 CYS cc_start: 0.6896 (m) cc_final: 0.6535 (m) REVERT: A 206 ARG cc_start: 0.9183 (mtm-85) cc_final: 0.8058 (tpm170) REVERT: A 216 SER cc_start: 0.9434 (t) cc_final: 0.9220 (p) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.1165 time to fit residues: 3.7901 Evaluate side-chains 29 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.073274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.055932 restraints weight = 14259.713| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.40 r_work: 0.2556 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2438 Z= 0.119 Angle : 0.518 3.808 3346 Z= 0.267 Chirality : 0.042 0.207 406 Planarity : 0.003 0.030 391 Dihedral : 6.967 51.938 567 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.02 % Allowed : 7.29 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.77 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.14 (0.50), residues: 93 loop : -0.90 (0.50), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 273 TYR 0.010 0.001 TYR A 212 PHE 0.011 0.001 PHE A 74 TRP 0.004 0.001 TRP A 174 HIS 0.002 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 2422) covalent geometry : angle 0.49574 ( 3301) SS BOND : bond 0.00313 ( 3) SS BOND : angle 1.36379 ( 6) hydrogen bonds : bond 0.02953 ( 73) hydrogen bonds : angle 5.48709 ( 192) link_ALPHA1-3 : bond 0.00873 ( 1) link_ALPHA1-3 : angle 1.50426 ( 3) link_ALPHA1-6 : bond 0.00945 ( 1) link_ALPHA1-6 : angle 1.82544 ( 3) link_BETA1-4 : bond 0.00179 ( 3) link_BETA1-4 : angle 1.38521 ( 9) link_NAG-ASN : bond 0.00128 ( 8) link_NAG-ASN : angle 1.29937 ( 24) *********************** 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 32 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9077 (p0) cc_final: 0.8837 (p0) REVERT: A 54 ARG cc_start: 0.8998 (mtt180) cc_final: 0.7802 (mtp85) REVERT: A 61 ILE cc_start: 0.8894 (mm) cc_final: 0.8612 (mm) REVERT: A 163 CYS cc_start: 0.6878 (m) cc_final: 0.6477 (m) REVERT: A 206 ARG cc_start: 0.9076 (mtm-85) cc_final: 0.8054 (tpm170) REVERT: A 216 SER cc_start: 0.9427 (t) cc_final: 0.9209 (p) outliers start: 5 outliers final: 4 residues processed: 28 average time/residue: 0.1502 time to fit residues: 5.0137 Evaluate side-chains 30 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3075 r_free = 0.3075 target = 0.073934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.057065 restraints weight = 14511.598| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.39 r_work: 0.2569 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2438 Z= 0.125 Angle : 0.550 7.336 3346 Z= 0.284 Chirality : 0.042 0.189 406 Planarity : 0.003 0.030 391 Dihedral : 6.825 52.615 567 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.21 % Allowed : 7.69 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.77 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.17 (0.50), residues: 91 loop : -0.91 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 273 TYR 0.010 0.001 TYR A 212 PHE 0.011 0.001 PHE A 74 TRP 0.007 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 2422) covalent geometry : angle 0.52532 ( 3301) SS BOND : bond 0.01648 ( 3) SS BOND : angle 2.10030 ( 6) hydrogen bonds : bond 0.02929 ( 73) hydrogen bonds : angle 5.36728 ( 192) link_ALPHA1-3 : bond 0.00841 ( 1) link_ALPHA1-3 : angle 1.49462 ( 3) link_ALPHA1-6 : bond 0.00847 ( 1) link_ALPHA1-6 : angle 1.68269 ( 3) link_BETA1-4 : bond 0.00180 ( 3) link_BETA1-4 : angle 1.42107 ( 9) link_NAG-ASN : bond 0.00148 ( 8) link_NAG-ASN : angle 1.31708 ( 24) ********************** 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 30 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 54 ARG cc_start: 0.9038 (mtt180) cc_final: 0.7788 (mtp85) REVERT: A 61 ILE cc_start: 0.8870 (mm) cc_final: 0.8588 (mm) REVERT: A 156 CYS cc_start: 0.8271 (m) cc_final: 0.8018 (m) REVERT: A 163 CYS cc_start: 0.6872 (m) cc_final: 0.6480 (m) REVERT: A 206 ARG cc_start: 0.9139 (mtm-85) cc_final: 0.8159 (tpt170) REVERT: A 216 SER cc_start: 0.9419 (t) cc_final: 0.9197 (p) outliers start: 3 outliers final: 3 residues processed: 27 average time/residue: 0.1557 time to fit residues: 4.9465 Evaluate side-chains 32 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 213 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.073504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.056359 restraints weight = 14510.335| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.42 r_work: 0.2571 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2438 Z= 0.125 Angle : 0.527 7.618 3346 Z= 0.271 Chirality : 0.041 0.132 406 Planarity : 0.003 0.031 391 Dihedral : 6.909 55.243 567 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.21 % Allowed : 7.69 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.77 (0.52), residues: 266 helix: None (None), residues: 0 sheet: 0.17 (0.50), residues: 91 loop : -0.92 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 273 TYR 0.011 0.001 TYR A 212 PHE 0.011 0.001 PHE A 74 TRP 0.008 0.001 TRP A 174 HIS 0.002 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 2422) covalent geometry : angle 0.50534 ( 3301) SS BOND : bond 0.01236 ( 3) SS BOND : angle 1.65710 ( 6) hydrogen bonds : bond 0.02903 ( 73) hydrogen bonds : angle 5.23365 ( 192) link_ALPHA1-3 : bond 0.00812 ( 1) link_ALPHA1-3 : angle 1.48441 ( 3) link_ALPHA1-6 : bond 0.00676 ( 1) link_ALPHA1-6 : angle 1.31526 ( 3) link_BETA1-4 : bond 0.00168 ( 3) link_BETA1-4 : angle 1.45979 ( 9) link_NAG-ASN : bond 0.00147 ( 8) link_NAG-ASN : angle 1.27268 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1692.93 seconds wall clock time: 29 minutes 24.92 seconds (1764.92 seconds total)