Starting phenix.real_space_refine on Thu Jun 5 01:02:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n17_48808/06_2025/9n17_48808_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n17_48808/06_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_48808/06_2025/9n17_48808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n17_48808/06_2025/9n17_48808.map" model { file = "/net/cci-nas-00/data/ceres_data/9n17_48808/06_2025/9n17_48808_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n17_48808/06_2025/9n17_48808_trim.cif" } resolution = 3.09 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= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 3.24, per 1000 atoms: 0.73 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: 1.46 Conformation dependent library (CDL) restraints added in 292.9 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, 45.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 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: 1.48 Time building geometry restraints manager: 1.65 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.440 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.850 ------------------------------------------------------------------------------- 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 (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: -1.34 (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 TRP 0.052 0.013 TRP A 197 HIS 0.007 0.004 HIS A 160 PHE 0.077 0.012 PHE A 74 TYR 0.084 0.014 TYR A 256 ARG 0.010 0.001 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00915 ( 8) link_NAG-ASN : angle 4.27323 ( 24) 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_ALPHA1-3 : bond 0.02323 ( 1) link_ALPHA1-3 : angle 2.52347 ( 3) hydrogen bonds : bond 0.11845 ( 73) hydrogen bonds : angle 8.05026 ( 192) SS BOND : bond 0.00613 ( 3) SS BOND : angle 2.09259 ( 6) covalent geometry : bond 0.01485 ( 2422) covalent geometry : angle 1.61710 ( 3301) *********************** 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 : 0.370 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: 0.7100 (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: 0.5844 time to fit residues: 28.8014 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 : 0.375 ------------------------------------------------------------------------------- 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 21 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3074 r_free = 0.3074 target = 0.072751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.055145 restraints weight = 13940.617| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 3.36 r_work: 0.2566 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2442 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= 0.179 Angle : 0.815 12.133 3346 Z= 0.421 Chirality : 0.048 0.326 406 Planarity : 0.004 0.031 391 Dihedral : 11.784 77.871 567 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % 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 (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: -0.95 (0.47), residues: 266 helix: None (None), residues: 0 sheet: 0.56 (0.50), residues: 96 loop : -1.43 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 174 HIS 0.002 0.001 HIS A 142 PHE 0.015 0.002 PHE A 74 TYR 0.020 0.001 TYR A 38 ARG 0.002 0.001 ARG A 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 8) link_NAG-ASN : angle 2.43795 ( 24) link_ALPHA1-6 : bond 0.00705 ( 1) link_ALPHA1-6 : angle 2.26386 ( 3) link_BETA1-4 : bond 0.00236 ( 3) link_BETA1-4 : angle 2.02136 ( 9) link_ALPHA1-3 : bond 0.01264 ( 1) link_ALPHA1-3 : angle 2.48610 ( 3) hydrogen bonds : bond 0.04301 ( 73) hydrogen bonds : angle 7.19404 ( 192) SS BOND : bond 0.00831 ( 3) SS BOND : angle 3.49292 ( 6) covalent geometry : bond 0.00424 ( 2422) covalent geometry : angle 0.76567 ( 3301) *********************** 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 : 0.358 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8304 (mt-10) REVERT: A 54 ARG cc_start: 0.8848 (mtt180) cc_final: 0.7390 (mmm160) REVERT: A 104 SER cc_start: 0.9668 (m) cc_final: 0.9336 (p) REVERT: A 120 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8264 (mm-30) REVERT: A 163 CYS cc_start: 0.7140 (m) cc_final: 0.6756 (m) REVERT: A 206 ARG cc_start: 0.9021 (mtm-85) cc_final: 0.8066 (tpt170) REVERT: A 216 SER cc_start: 0.9371 (t) cc_final: 0.9161 (p) outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 0.4153 time to fit residues: 14.2897 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 : 0.346 ------------------------------------------------------------------------------- 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 7 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3052 r_free = 0.3052 target = 0.072131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.054884 restraints weight = 14171.688| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 3.37 r_work: 0.2540 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 2438 Z= 0.160 Angle : 0.683 8.794 3346 Z= 0.355 Chirality : 0.045 0.200 406 Planarity : 0.004 0.035 391 Dihedral : 10.847 70.052 567 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.40 % Allowed : 7.29 % 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 (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: -0.80 (0.49), residues: 266 helix: None (None), residues: 0 sheet: 0.35 (0.51), residues: 93 loop : -1.08 (0.46), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 PHE 0.018 0.002 PHE A 74 TYR 0.016 0.001 TYR A 38 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 8) link_NAG-ASN : angle 1.73370 ( 24) link_ALPHA1-6 : bond 0.00549 ( 1) link_ALPHA1-6 : angle 2.01533 ( 3) link_BETA1-4 : bond 0.00234 ( 3) link_BETA1-4 : angle 1.38100 ( 9) link_ALPHA1-3 : bond 0.01117 ( 1) link_ALPHA1-3 : angle 1.59610 ( 3) hydrogen bonds : bond 0.03706 ( 73) hydrogen bonds : angle 6.64147 ( 192) SS BOND : bond 0.00669 ( 3) SS BOND : angle 3.59279 ( 6) covalent geometry : bond 0.00378 ( 2422) covalent geometry : angle 0.64571 ( 3301) *********************** 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 : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8373 (mt-10) REVERT: A 54 ARG cc_start: 0.8892 (mtt180) cc_final: 0.7502 (mtp85) REVERT: A 163 CYS cc_start: 0.6890 (m) cc_final: 0.6610 (m) REVERT: A 206 ARG cc_start: 0.9163 (mtm-85) cc_final: 0.8093 (tpt170) REVERT: A 216 SER cc_start: 0.9351 (t) cc_final: 0.9147 (p) outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.4487 time to fit residues: 13.3594 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 : 0.346 ------------------------------------------------------------------------------- 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 10 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3039 r_free = 0.3039 target = 0.071606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.054336 restraints weight = 14386.248| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 3.34 r_work: 0.2538 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 2438 Z= 0.168 Angle : 0.610 5.216 3346 Z= 0.312 Chirality : 0.044 0.240 406 Planarity : 0.004 0.033 391 Dihedral : 9.368 56.711 567 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.81 % Allowed : 6.48 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.04 (0.48), residues: 266 helix: None (None), residues: 0 sheet: 0.10 (0.50), residues: 93 loop : -1.18 (0.45), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 174 HIS 0.002 0.000 HIS A 201 PHE 0.017 0.001 PHE A 74 TYR 0.013 0.001 TYR A 38 ARG 0.003 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 8) link_NAG-ASN : angle 1.63974 ( 24) link_ALPHA1-6 : bond 0.00786 ( 1) link_ALPHA1-6 : angle 2.02123 ( 3) link_BETA1-4 : bond 0.00115 ( 3) link_BETA1-4 : angle 1.32357 ( 9) link_ALPHA1-3 : bond 0.01078 ( 1) link_ALPHA1-3 : angle 1.74130 ( 3) hydrogen bonds : bond 0.03356 ( 73) hydrogen bonds : angle 6.24360 ( 192) SS BOND : bond 0.01301 ( 3) SS BOND : angle 3.08806 ( 6) covalent geometry : bond 0.00377 ( 2422) covalent geometry : angle 0.57322 ( 3301) *********************** 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 : 0.387 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8352 (mt-10) REVERT: A 54 ARG cc_start: 0.8958 (mtt180) cc_final: 0.7712 (mtp85) REVERT: A 61 ILE cc_start: 0.8963 (mm) cc_final: 0.8690 (mm) REVERT: A 163 CYS cc_start: 0.6970 (m) cc_final: 0.6587 (m) REVERT: A 206 ARG cc_start: 0.9248 (mtm-85) cc_final: 0.7964 (tpp-160) REVERT: A 216 SER cc_start: 0.9429 (t) cc_final: 0.9208 (p) outliers start: 2 outliers final: 1 residues processed: 26 average time/residue: 0.4587 time to fit residues: 14.1715 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 : 0.387 ------------------------------------------------------------------------------- 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 21 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3047 r_free = 0.3047 target = 0.072414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.055758 restraints weight = 14464.033| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.31 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: 0.8240 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2438 Z= 0.139 Angle : 0.565 5.365 3346 Z= 0.289 Chirality : 0.043 0.238 406 Planarity : 0.004 0.033 391 Dihedral : 8.721 51.885 567 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.62 % Allowed : 6.88 % 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 (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: -0.97 (0.49), residues: 266 helix: None (None), residues: 0 sheet: 0.17 (0.50), residues: 93 loop : -1.15 (0.46), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 PHE 0.014 0.001 PHE A 74 TYR 0.011 0.001 TYR A 212 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00152 ( 8) link_NAG-ASN : angle 1.42599 ( 24) link_ALPHA1-6 : bond 0.00847 ( 1) link_ALPHA1-6 : angle 1.97771 ( 3) link_BETA1-4 : bond 0.00160 ( 3) link_BETA1-4 : angle 1.29353 ( 9) link_ALPHA1-3 : bond 0.01096 ( 1) link_ALPHA1-3 : angle 1.69483 ( 3) hydrogen bonds : bond 0.03190 ( 73) hydrogen bonds : angle 6.02368 ( 192) SS BOND : bond 0.00263 ( 3) SS BOND : angle 2.01158 ( 6) covalent geometry : bond 0.00313 ( 2422) covalent geometry : angle 0.53922 ( 3301) *********************** 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: 4 poor density : 26 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8415 (mt-10) REVERT: A 54 ARG cc_start: 0.8981 (mtt180) cc_final: 0.7741 (mtp85) REVERT: A 61 ILE cc_start: 0.8966 (mm) cc_final: 0.8700 (mm) REVERT: A 163 CYS cc_start: 0.6988 (m) cc_final: 0.6599 (m) REVERT: A 206 ARG cc_start: 0.9209 (mtm-85) cc_final: 0.8093 (tpt170) REVERT: A 216 SER cc_start: 0.9416 (t) cc_final: 0.9203 (p) outliers start: 4 outliers final: 4 residues processed: 26 average time/residue: 0.3169 time to fit residues: 9.8077 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 : 0.330 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3036 r_free = 0.3036 target = 0.072033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.055160 restraints weight = 14429.169| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 3.34 r_work: 0.2521 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2438 Z= 0.195 Angle : 0.567 4.313 3346 Z= 0.289 Chirality : 0.043 0.246 406 Planarity : 0.004 0.031 391 Dihedral : 7.979 49.856 567 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.02 % Allowed : 6.48 % 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 (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: -0.99 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.14 (0.51), residues: 93 loop : -1.15 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 174 HIS 0.003 0.000 HIS A 201 PHE 0.015 0.001 PHE A 74 TYR 0.011 0.001 TYR A 38 ARG 0.001 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 8) link_NAG-ASN : angle 1.50185 ( 24) link_ALPHA1-6 : bond 0.00950 ( 1) link_ALPHA1-6 : angle 1.92703 ( 3) link_BETA1-4 : bond 0.00128 ( 3) link_BETA1-4 : angle 1.38362 ( 9) link_ALPHA1-3 : bond 0.00946 ( 1) link_ALPHA1-3 : angle 1.65694 ( 3) hydrogen bonds : bond 0.03237 ( 73) hydrogen bonds : angle 5.92691 ( 192) SS BOND : bond 0.00168 ( 3) SS BOND : angle 1.85394 ( 6) covalent geometry : bond 0.00425 ( 2422) covalent geometry : angle 0.54083 ( 3301) *********************** 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 31 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 54 ARG cc_start: 0.9008 (mtt180) cc_final: 0.7771 (mtp85) REVERT: A 61 ILE cc_start: 0.8901 (mm) cc_final: 0.8634 (mm) REVERT: A 163 CYS cc_start: 0.7005 (m) cc_final: 0.6639 (m) REVERT: A 206 ARG cc_start: 0.9203 (mtm-85) cc_final: 0.8070 (tpm170) REVERT: A 216 SER cc_start: 0.9434 (t) cc_final: 0.9217 (p) REVERT: A 252 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8757 (mm-30) outliers start: 5 outliers final: 5 residues processed: 26 average time/residue: 0.3157 time to fit residues: 9.7912 Evaluate side-chains 30 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 180 GLU 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 3 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 0 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3055 r_free = 0.3055 target = 0.072829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.055181 restraints weight = 14524.898| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 3.47 r_work: 0.2539 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2438 Z= 0.100 Angle : 0.558 6.394 3346 Z= 0.286 Chirality : 0.044 0.227 406 Planarity : 0.003 0.032 391 Dihedral : 7.579 49.831 567 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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 (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: -0.92 (0.50), residues: 266 helix: None (None), residues: 0 sheet: 0.12 (0.50), residues: 93 loop : -1.06 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 174 HIS 0.002 0.000 HIS A 201 PHE 0.012 0.001 PHE A 74 TYR 0.011 0.001 TYR A 212 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00116 ( 8) link_NAG-ASN : angle 1.30550 ( 24) link_ALPHA1-6 : bond 0.00924 ( 1) link_ALPHA1-6 : angle 1.90116 ( 3) link_BETA1-4 : bond 0.00236 ( 3) link_BETA1-4 : angle 1.28702 ( 9) link_ALPHA1-3 : bond 0.00982 ( 1) link_ALPHA1-3 : angle 1.54358 ( 3) hydrogen bonds : bond 0.02926 ( 73) hydrogen bonds : angle 5.61619 ( 192) SS BOND : bond 0.01319 ( 3) SS BOND : angle 2.66990 ( 6) covalent geometry : bond 0.00222 ( 2422) covalent geometry : angle 0.52899 ( 3301) *********************** 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: 3 poor density : 27 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9101 (p0) cc_final: 0.8887 (p0) REVERT: A 54 ARG cc_start: 0.8973 (mtt180) cc_final: 0.7786 (mtp85) REVERT: A 61 ILE cc_start: 0.8904 (mm) cc_final: 0.8634 (mm) REVERT: A 156 CYS cc_start: 0.8096 (m) cc_final: 0.7825 (m) REVERT: A 163 CYS cc_start: 0.6920 (m) cc_final: 0.6531 (m) REVERT: A 206 ARG cc_start: 0.9190 (mtm-85) cc_final: 0.8095 (tpt170) REVERT: A 216 SER cc_start: 0.9416 (t) cc_final: 0.9198 (p) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.3058 time to fit residues: 9.9400 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 : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS 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 3 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3075 r_free = 0.3075 target = 0.073657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.056116 restraints weight = 14303.412| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 3.47 r_work: 0.2551 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 2438 Z= 0.110 Angle : 0.529 5.843 3346 Z= 0.271 Chirality : 0.043 0.215 406 Planarity : 0.003 0.032 391 Dihedral : 6.999 51.905 567 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.81 % Allowed : 8.50 % 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 (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: -0.90 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.16 (0.51), residues: 91 loop : -1.05 (0.48), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 PHE 0.011 0.001 PHE A 74 TYR 0.010 0.001 TYR A 212 ARG 0.001 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 8) link_NAG-ASN : angle 1.33348 ( 24) link_ALPHA1-6 : bond 0.00989 ( 1) link_ALPHA1-6 : angle 1.80582 ( 3) link_BETA1-4 : bond 0.00202 ( 3) link_BETA1-4 : angle 1.37253 ( 9) link_ALPHA1-3 : bond 0.00895 ( 1) link_ALPHA1-3 : angle 1.55323 ( 3) hydrogen bonds : bond 0.02873 ( 73) hydrogen bonds : angle 5.41007 ( 192) SS BOND : bond 0.01079 ( 3) SS BOND : angle 2.01053 ( 6) covalent geometry : bond 0.00245 ( 2422) covalent geometry : angle 0.50313 ( 3301) *********************** 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 28 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9094 (p0) cc_final: 0.8890 (p0) REVERT: A 54 ARG cc_start: 0.8995 (mtt180) cc_final: 0.7780 (mtp85) REVERT: A 61 ILE cc_start: 0.8877 (mm) cc_final: 0.8596 (mm) REVERT: A 163 CYS cc_start: 0.6865 (m) cc_final: 0.6470 (m) REVERT: A 206 ARG cc_start: 0.9190 (mtm-85) cc_final: 0.8033 (tpm170) REVERT: A 216 SER cc_start: 0.9413 (t) cc_final: 0.9193 (p) outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.3160 time to fit residues: 9.8372 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 : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS 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 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 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 = 0.3087 r_free = 0.3087 target = 0.074483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.057757 restraints weight = 14345.585| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.37 r_work: 0.2557 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2438 Z= 0.108 Angle : 0.519 5.459 3346 Z= 0.265 Chirality : 0.042 0.197 406 Planarity : 0.003 0.031 391 Dihedral : 6.758 52.911 567 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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 (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: -0.82 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.19 (0.50), residues: 91 loop : -0.98 (0.48), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 PHE 0.010 0.001 PHE A 74 TYR 0.010 0.001 TYR A 212 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 8) link_NAG-ASN : angle 1.30103 ( 24) link_ALPHA1-6 : bond 0.00901 ( 1) link_ALPHA1-6 : angle 1.75799 ( 3) link_BETA1-4 : bond 0.00240 ( 3) link_BETA1-4 : angle 1.38955 ( 9) link_ALPHA1-3 : bond 0.00836 ( 1) link_ALPHA1-3 : angle 1.51207 ( 3) hydrogen bonds : bond 0.02851 ( 73) hydrogen bonds : angle 5.29814 ( 192) SS BOND : bond 0.01253 ( 3) SS BOND : angle 1.60256 ( 6) covalent geometry : bond 0.00237 ( 2422) covalent geometry : angle 0.49559 ( 3301) *********************** 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 : 0.372 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9083 (p0) cc_final: 0.8870 (p0) REVERT: A 54 ARG cc_start: 0.9029 (mtt180) cc_final: 0.7776 (mtp85) REVERT: A 61 ILE cc_start: 0.8841 (mm) cc_final: 0.8556 (mm) REVERT: A 163 CYS cc_start: 0.6861 (m) cc_final: 0.6456 (m) REVERT: A 206 ARG cc_start: 0.9183 (mtm-85) cc_final: 0.8065 (tpm170) REVERT: A 216 SER cc_start: 0.9409 (t) cc_final: 0.9182 (p) outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.3178 time to fit residues: 9.9268 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 : 0.354 ------------------------------------------------------------------------------- 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 2 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 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 = 0.3101 r_free = 0.3101 target = 0.075109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.058324 restraints weight = 14349.150| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 3.39 r_work: 0.2575 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2438 Z= 0.102 Angle : 0.507 5.197 3346 Z= 0.261 Chirality : 0.042 0.149 406 Planarity : 0.003 0.032 391 Dihedral : 6.661 53.847 567 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.81 % Allowed : 8.10 % 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 (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: -0.78 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.15 (0.49), residues: 93 loop : -0.92 (0.49), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 174 HIS 0.002 0.000 HIS A 201 PHE 0.009 0.001 PHE A 74 TYR 0.011 0.001 TYR A 212 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 8) link_NAG-ASN : angle 1.24672 ( 24) link_ALPHA1-6 : bond 0.00761 ( 1) link_ALPHA1-6 : angle 1.44248 ( 3) link_BETA1-4 : bond 0.00225 ( 3) link_BETA1-4 : angle 1.43548 ( 9) link_ALPHA1-3 : bond 0.00819 ( 1) link_ALPHA1-3 : angle 1.49766 ( 3) hydrogen bonds : bond 0.02785 ( 73) hydrogen bonds : angle 5.18412 ( 192) SS BOND : bond 0.00812 ( 3) SS BOND : angle 1.47831 ( 6) covalent geometry : bond 0.00228 ( 2422) covalent geometry : angle 0.48551 ( 3301) ********************** 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: 2 poor density : 28 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 54 ARG cc_start: 0.9047 (mtt180) cc_final: 0.7819 (mtp85) REVERT: A 61 ILE cc_start: 0.8852 (mm) cc_final: 0.8562 (mm) REVERT: A 163 CYS cc_start: 0.6901 (m) cc_final: 0.6466 (m) REVERT: A 206 ARG cc_start: 0.9185 (mtm-85) cc_final: 0.8074 (tpm170) REVERT: A 216 SER cc_start: 0.9400 (t) cc_final: 0.9175 (p) outliers start: 2 outliers final: 2 residues processed: 28 average time/residue: 0.3000 time to fit residues: 10.1499 Evaluate side-chains 31 residues out of total 247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS 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 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3087 r_free = 0.3087 target = 0.074238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.056769 restraints weight = 14480.210| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 3.47 r_work: 0.2578 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2438 Z= 0.112 Angle : 0.501 5.219 3346 Z= 0.258 Chirality : 0.041 0.130 406 Planarity : 0.003 0.032 391 Dihedral : 6.758 56.950 567 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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 (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: -0.81 (0.51), residues: 266 helix: None (None), residues: 0 sheet: 0.16 (0.50), residues: 91 loop : -0.94 (0.49), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 174 HIS 0.002 0.001 HIS A 201 PHE 0.009 0.001 PHE A 74 TYR 0.011 0.001 TYR A 212 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 8) link_NAG-ASN : angle 1.26125 ( 24) link_ALPHA1-6 : bond 0.00539 ( 1) link_ALPHA1-6 : angle 1.51599 ( 3) link_BETA1-4 : bond 0.00158 ( 3) link_BETA1-4 : angle 1.43296 ( 9) link_ALPHA1-3 : bond 0.00728 ( 1) link_ALPHA1-3 : angle 1.50636 ( 3) hydrogen bonds : bond 0.02792 ( 73) hydrogen bonds : angle 5.10284 ( 192) SS BOND : bond 0.00851 ( 3) SS BOND : angle 1.47982 ( 6) covalent geometry : bond 0.00250 ( 2422) covalent geometry : angle 0.47816 ( 3301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3318.44 seconds wall clock time: 57 minutes 24.28 seconds (3444.28 seconds total)