Starting phenix.real_space_refine on Wed Jul 23 07:50:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dbe_46716/07_2025/9dbe_46716.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dbe_46716/07_2025/9dbe_46716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dbe_46716/07_2025/9dbe_46716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dbe_46716/07_2025/9dbe_46716.map" model { file = "/net/cci-nas-00/data/ceres_data/9dbe_46716/07_2025/9dbe_46716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dbe_46716/07_2025/9dbe_46716.cif" } resolution = 2.4 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= -0.000 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 1348 2.51 5 N 336 2.21 5 O 457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 2150 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1920 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 237} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 42 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1, 'water': 28} Link IDs: {None: 28} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.75, per 1000 atoms: 2.21 Number of scatterers: 2150 At special positions: 0 Unit cell: (66.5016, 65.494, 65.494, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 457 8.00 N 336 7.00 C 1348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 68 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 160 " distance=2.04 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 260 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 3 " NAG-ASN " NAG A1501 " - " ASN A 236 " " NAG B 1 " - " ASN A 176 " " NAG C 1 " - " ASN A 210 " " NAG D 1 " - " ASN A 243 " " NAG E 1 " - " ASN A 29 " " NAG F 1 " - " ASN A 95 " " NAG G 1 " - " ASN A 67 " Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 270.6 milliseconds 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 458 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 11.0% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 38 through 45 removed outlier: 3.662A pdb=" N PHE A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.831A pdb=" N CYS A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 58 removed outlier: 4.561A pdb=" N TYR A 239 " --> pdb=" O CYS A 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 81 removed outlier: 6.943A pdb=" N ALA A 76 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE A 208 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N GLU A 112 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASN A 210 " --> pdb=" O HIS A 110 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 106 " --> pdb=" O MET A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 202 76 hydrogen bonds defined for protein. 192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.61 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 621 1.34 - 1.46: 577 1.46 - 1.58: 967 1.58 - 1.70: 0 1.70 - 1.82: 12 Bond restraints: 2177 Sorted by residual: bond pdb=" C VAL A 167 " pdb=" O VAL A 167 " ideal model delta sigma weight residual 1.232 1.240 -0.009 1.01e-02 9.80e+03 7.22e-01 bond pdb=" N VAL A 167 " pdb=" CA VAL A 167 " ideal model delta sigma weight residual 1.456 1.461 -0.005 8.60e-03 1.35e+04 3.14e-01 bond pdb=" C VAL A 171 " pdb=" N ILE A 172 " ideal model delta sigma weight residual 1.329 1.324 0.006 1.13e-02 7.83e+03 2.45e-01 bond pdb=" C LYS A 166 " pdb=" N VAL A 167 " ideal model delta sigma weight residual 1.326 1.330 -0.004 9.20e-03 1.18e+04 2.32e-01 bond pdb=" CA THR A 238 " pdb=" CB THR A 238 " ideal model delta sigma weight residual 1.533 1.544 -0.011 2.29e-02 1.91e+03 2.28e-01 ... (remaining 2172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 2851 1.28 - 2.56: 105 2.56 - 3.84: 16 3.84 - 5.12: 2 5.12 - 6.39: 1 Bond angle restraints: 2975 Sorted by residual: angle pdb=" N VAL A 171 " pdb=" CA VAL A 171 " pdb=" C VAL A 171 " ideal model delta sigma weight residual 109.34 104.79 4.55 2.08e+00 2.31e-01 4.78e+00 angle pdb=" C GLN A 128 " pdb=" N HIS A 129 " pdb=" CA HIS A 129 " ideal model delta sigma weight residual 121.54 125.23 -3.69 1.91e+00 2.74e-01 3.73e+00 angle pdb=" CA CYS A 260 " pdb=" CB CYS A 260 " pdb=" SG CYS A 260 " ideal model delta sigma weight residual 114.40 118.75 -4.35 2.30e+00 1.89e-01 3.58e+00 angle pdb=" N VAL A 167 " pdb=" CA VAL A 167 " pdb=" C VAL A 167 " ideal model delta sigma weight residual 108.15 109.98 -1.83 9.90e-01 1.02e+00 3.43e+00 angle pdb=" N GLY A 182 " pdb=" CA GLY A 182 " pdb=" C GLY A 182 " ideal model delta sigma weight residual 111.14 114.37 -3.23 1.80e+00 3.09e-01 3.21e+00 ... (remaining 2970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.10: 1286 12.10 - 24.19: 94 24.19 - 36.29: 41 36.29 - 48.38: 11 48.38 - 60.48: 4 Dihedral angle restraints: 1436 sinusoidal: 715 harmonic: 721 Sorted by residual: dihedral pdb=" CA SER A 170 " pdb=" C SER A 170 " pdb=" N VAL A 171 " pdb=" CA VAL A 171 " ideal model delta harmonic sigma weight residual 180.00 157.03 22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA TRP A 185 " pdb=" C TRP A 185 " pdb=" N ASN A 186 " pdb=" CA ASN A 186 " ideal model delta harmonic sigma weight residual 180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA TYR A 229 " pdb=" C TYR A 229 " pdb=" N VAL A 230 " pdb=" CA VAL A 230 " ideal model delta harmonic sigma weight residual 180.00 164.82 15.18 0 5.00e+00 4.00e-02 9.22e+00 ... (remaining 1433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 202 0.029 - 0.058: 97 0.058 - 0.086: 40 0.086 - 0.115: 23 0.115 - 0.144: 7 Chirality restraints: 369 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 176 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA VAL A 171 " pdb=" N VAL A 171 " pdb=" C VAL A 171 " pdb=" CB VAL A 171 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 67 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 366 not shown) Planarity restraints: 365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 112 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.36e+00 pdb=" N PRO A 113 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 103 " -0.016 5.00e-02 4.00e+02 2.37e-02 9.02e-01 pdb=" N PRO A 104 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 107 " 0.008 2.00e-02 2.50e+03 6.80e-03 8.09e-01 pdb=" CG PHE A 107 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE A 107 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 107 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 107 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 107 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 107 " 0.003 2.00e-02 2.50e+03 ... (remaining 362 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 430 2.79 - 3.31: 1715 3.31 - 3.84: 3507 3.84 - 4.37: 4272 4.37 - 4.90: 7090 Nonbonded interactions: 17014 Sorted by model distance: nonbonded pdb=" OG SER A 170 " pdb=" O VAL A 171 " model vdw 2.258 3.040 nonbonded pdb=" O5 NAG D 2 " pdb=" O6 NAG D 2 " model vdw 2.443 2.432 nonbonded pdb=" O5 NAG E 1 " pdb=" O6 NAG E 1 " model vdw 2.505 2.432 nonbonded pdb=" N VAL A 171 " pdb=" O VAL A 171 " model vdw 2.545 2.496 nonbonded pdb=" O ALA A 122 " pdb=" NH2 ARG A 130 " model vdw 2.565 3.120 ... (remaining 17009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 13.940 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2195 Z= 0.136 Angle : 0.622 6.395 3026 Z= 0.316 Chirality : 0.045 0.144 369 Planarity : 0.003 0.029 358 Dihedral : 10.735 60.479 969 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.51 % Allowed : 5.53 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.06 (0.53), residues: 243 helix: -1.84 (1.16), residues: 14 sheet: 0.96 (0.49), residues: 96 loop : -0.41 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 207 HIS 0.004 0.001 HIS A 110 PHE 0.015 0.002 PHE A 107 TYR 0.008 0.001 TYR A 240 ARG 0.003 0.001 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 7) link_NAG-ASN : angle 1.92970 ( 21) link_BETA1-4 : bond 0.00372 ( 6) link_BETA1-4 : angle 1.66602 ( 18) hydrogen bonds : bond 0.14064 ( 76) hydrogen bonds : angle 6.19963 ( 192) link_BETA1-6 : bond 0.00344 ( 2) link_BETA1-6 : angle 1.13384 ( 6) SS BOND : bond 0.00640 ( 3) SS BOND : angle 0.74902 ( 6) covalent geometry : bond 0.00288 ( 2177) covalent geometry : angle 0.58906 ( 2975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.255 Fit side-chains REVERT: A 231 TYR cc_start: 0.9286 (OUTLIER) cc_final: 0.8821 (p90) outliers start: 3 outliers final: 1 residues processed: 34 average time/residue: 1.4606 time to fit residues: 50.6709 Evaluate side-chains 30 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 231 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 36 ASN A 135 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.105724 restraints weight = 2173.980| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.66 r_work: 0.3037 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2195 Z= 0.198 Angle : 0.712 6.762 3026 Z= 0.362 Chirality : 0.048 0.149 369 Planarity : 0.004 0.031 358 Dihedral : 7.060 44.687 579 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.52 % Allowed : 10.55 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.02 (0.53), residues: 243 helix: -2.24 (1.11), residues: 14 sheet: 0.90 (0.47), residues: 103 loop : -0.44 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 185 HIS 0.002 0.001 HIS A 84 PHE 0.015 0.003 PHE A 107 TYR 0.010 0.002 TYR A 215 ARG 0.005 0.001 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 7) link_NAG-ASN : angle 2.07436 ( 21) link_BETA1-4 : bond 0.00487 ( 6) link_BETA1-4 : angle 1.78322 ( 18) hydrogen bonds : bond 0.05930 ( 76) hydrogen bonds : angle 5.87459 ( 192) link_BETA1-6 : bond 0.00370 ( 2) link_BETA1-6 : angle 1.08666 ( 6) SS BOND : bond 0.00544 ( 3) SS BOND : angle 0.85049 ( 6) covalent geometry : bond 0.00451 ( 2177) covalent geometry : angle 0.67961 ( 2975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.245 Fit side-chains REVERT: A 231 TYR cc_start: 0.9305 (OUTLIER) cc_final: 0.8753 (p90) REVERT: A 237 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8621 (t80) outliers start: 7 outliers final: 2 residues processed: 35 average time/residue: 1.4182 time to fit residues: 50.6482 Evaluate side-chains 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 20 optimal weight: 0.3980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.127682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.106780 restraints weight = 2138.779| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.58 r_work: 0.3050 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2195 Z= 0.157 Angle : 0.658 7.024 3026 Z= 0.333 Chirality : 0.047 0.144 369 Planarity : 0.004 0.030 358 Dihedral : 6.751 45.253 579 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.01 % Allowed : 12.56 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.09 (0.53), residues: 243 helix: -2.17 (1.12), residues: 14 sheet: 0.91 (0.47), residues: 103 loop : -0.35 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 207 HIS 0.002 0.001 HIS A 110 PHE 0.015 0.002 PHE A 107 TYR 0.011 0.002 TYR A 215 ARG 0.003 0.001 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 7) link_NAG-ASN : angle 2.00276 ( 21) link_BETA1-4 : bond 0.00423 ( 6) link_BETA1-4 : angle 1.73560 ( 18) hydrogen bonds : bond 0.05328 ( 76) hydrogen bonds : angle 5.85766 ( 192) link_BETA1-6 : bond 0.00357 ( 2) link_BETA1-6 : angle 1.09218 ( 6) SS BOND : bond 0.00561 ( 3) SS BOND : angle 0.89952 ( 6) covalent geometry : bond 0.00347 ( 2177) covalent geometry : angle 0.62407 ( 2975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.222 Fit side-chains REVERT: A 213 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9112 (tp) REVERT: A 231 TYR cc_start: 0.9311 (OUTLIER) cc_final: 0.8767 (p90) REVERT: A 237 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8581 (t80) outliers start: 4 outliers final: 1 residues processed: 33 average time/residue: 1.4424 time to fit residues: 48.5503 Evaluate side-chains 33 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.106038 restraints weight = 2110.783| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.61 r_work: 0.3044 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2195 Z= 0.169 Angle : 0.672 6.988 3026 Z= 0.340 Chirality : 0.047 0.150 369 Planarity : 0.004 0.030 358 Dihedral : 6.647 45.800 578 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.52 % Allowed : 12.56 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.03 (0.53), residues: 243 helix: -2.31 (1.07), residues: 14 sheet: 0.98 (0.49), residues: 98 loop : -0.43 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 185 HIS 0.002 0.001 HIS A 110 PHE 0.015 0.002 PHE A 107 TYR 0.011 0.002 TYR A 215 ARG 0.003 0.001 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 7) link_NAG-ASN : angle 2.05272 ( 21) link_BETA1-4 : bond 0.00444 ( 6) link_BETA1-4 : angle 1.75268 ( 18) hydrogen bonds : bond 0.05396 ( 76) hydrogen bonds : angle 5.87390 ( 192) link_BETA1-6 : bond 0.00458 ( 2) link_BETA1-6 : angle 1.08222 ( 6) SS BOND : bond 0.00532 ( 3) SS BOND : angle 0.82972 ( 6) covalent geometry : bond 0.00380 ( 2177) covalent geometry : angle 0.63812 ( 2975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.229 Fit side-chains REVERT: A 213 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9105 (tp) REVERT: A 231 TYR cc_start: 0.9323 (OUTLIER) cc_final: 0.8742 (p90) REVERT: A 237 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8602 (t80) outliers start: 7 outliers final: 1 residues processed: 35 average time/residue: 1.3937 time to fit residues: 49.8523 Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.127573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.106914 restraints weight = 2168.414| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.60 r_work: 0.3054 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2195 Z= 0.145 Angle : 0.638 7.046 3026 Z= 0.322 Chirality : 0.046 0.145 369 Planarity : 0.004 0.028 358 Dihedral : 6.400 45.869 578 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.51 % Allowed : 13.57 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.07 (0.53), residues: 243 helix: -2.14 (1.13), residues: 14 sheet: 0.99 (0.49), residues: 98 loop : -0.41 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 185 HIS 0.002 0.001 HIS A 110 PHE 0.015 0.002 PHE A 107 TYR 0.012 0.001 TYR A 215 ARG 0.003 0.001 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 7) link_NAG-ASN : angle 1.99952 ( 21) link_BETA1-4 : bond 0.00412 ( 6) link_BETA1-4 : angle 1.72861 ( 18) hydrogen bonds : bond 0.05060 ( 76) hydrogen bonds : angle 5.83157 ( 192) link_BETA1-6 : bond 0.00461 ( 2) link_BETA1-6 : angle 1.09436 ( 6) SS BOND : bond 0.00515 ( 3) SS BOND : angle 0.87742 ( 6) covalent geometry : bond 0.00320 ( 2177) covalent geometry : angle 0.60289 ( 2975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.245 Fit side-chains REVERT: A 213 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9160 (tp) REVERT: A 231 TYR cc_start: 0.9319 (OUTLIER) cc_final: 0.8738 (p90) REVERT: A 237 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8564 (t80) outliers start: 5 outliers final: 0 residues processed: 32 average time/residue: 1.5340 time to fit residues: 50.0694 Evaluate side-chains 30 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107598 restraints weight = 2160.816| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.56 r_work: 0.3064 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2195 Z= 0.134 Angle : 0.619 6.753 3026 Z= 0.313 Chirality : 0.046 0.145 369 Planarity : 0.003 0.028 358 Dihedral : 6.193 46.075 578 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.52 % Allowed : 12.56 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.54), residues: 243 helix: -2.03 (1.15), residues: 14 sheet: 1.01 (0.49), residues: 98 loop : -0.36 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 207 HIS 0.002 0.001 HIS A 110 PHE 0.015 0.002 PHE A 107 TYR 0.012 0.001 TYR A 215 ARG 0.003 0.000 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 7) link_NAG-ASN : angle 1.94784 ( 21) link_BETA1-4 : bond 0.00407 ( 6) link_BETA1-4 : angle 1.70198 ( 18) hydrogen bonds : bond 0.04904 ( 76) hydrogen bonds : angle 5.79156 ( 192) link_BETA1-6 : bond 0.00461 ( 2) link_BETA1-6 : angle 1.09295 ( 6) SS BOND : bond 0.00438 ( 3) SS BOND : angle 0.86926 ( 6) covalent geometry : bond 0.00294 ( 2177) covalent geometry : angle 0.58434 ( 2975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.240 Fit side-chains REVERT: A 213 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9160 (tp) REVERT: A 231 TYR cc_start: 0.9319 (OUTLIER) cc_final: 0.8748 (p90) REVERT: A 237 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8535 (t80) outliers start: 7 outliers final: 1 residues processed: 34 average time/residue: 1.5035 time to fit residues: 52.1545 Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.106118 restraints weight = 2210.102| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.61 r_work: 0.3044 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2195 Z= 0.173 Angle : 0.671 7.235 3026 Z= 0.339 Chirality : 0.047 0.149 369 Planarity : 0.004 0.030 358 Dihedral : 6.366 46.490 578 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.52 % Allowed : 11.56 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.06 (0.53), residues: 243 helix: -2.15 (1.13), residues: 14 sheet: 1.02 (0.49), residues: 98 loop : -0.45 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 185 HIS 0.003 0.001 HIS A 110 PHE 0.015 0.002 PHE A 107 TYR 0.011 0.002 TYR A 215 ARG 0.003 0.001 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 7) link_NAG-ASN : angle 2.03886 ( 21) link_BETA1-4 : bond 0.00453 ( 6) link_BETA1-4 : angle 1.75152 ( 18) hydrogen bonds : bond 0.05348 ( 76) hydrogen bonds : angle 5.84159 ( 192) link_BETA1-6 : bond 0.00433 ( 2) link_BETA1-6 : angle 1.10777 ( 6) SS BOND : bond 0.00508 ( 3) SS BOND : angle 0.79710 ( 6) covalent geometry : bond 0.00390 ( 2177) covalent geometry : angle 0.63792 ( 2975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.242 Fit side-chains REVERT: A 213 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9138 (tp) REVERT: A 231 TYR cc_start: 0.9314 (OUTLIER) cc_final: 0.8770 (p90) REVERT: A 237 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8603 (t80) outliers start: 9 outliers final: 3 residues processed: 35 average time/residue: 1.4180 time to fit residues: 50.6343 Evaluate side-chains 31 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 0.4980 chunk 19 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107443 restraints weight = 2234.517| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.61 r_work: 0.3062 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2195 Z= 0.121 Angle : 0.603 6.797 3026 Z= 0.304 Chirality : 0.045 0.143 369 Planarity : 0.003 0.028 358 Dihedral : 6.011 46.109 578 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.02 % Allowed : 12.06 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.16 (0.54), residues: 243 helix: -1.87 (1.15), residues: 14 sheet: 1.01 (0.49), residues: 98 loop : -0.33 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 185 HIS 0.001 0.000 HIS A 110 PHE 0.014 0.002 PHE A 107 TYR 0.012 0.001 TYR A 215 ARG 0.002 0.000 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 7) link_NAG-ASN : angle 1.94156 ( 21) link_BETA1-4 : bond 0.00391 ( 6) link_BETA1-4 : angle 1.68275 ( 18) hydrogen bonds : bond 0.04706 ( 76) hydrogen bonds : angle 5.76633 ( 192) link_BETA1-6 : bond 0.00462 ( 2) link_BETA1-6 : angle 1.09261 ( 6) SS BOND : bond 0.00401 ( 3) SS BOND : angle 0.73208 ( 6) covalent geometry : bond 0.00261 ( 2177) covalent geometry : angle 0.56842 ( 2975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.239 Fit side-chains REVERT: A 231 TYR cc_start: 0.9320 (OUTLIER) cc_final: 0.8754 (p90) REVERT: A 237 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8498 (t80) outliers start: 8 outliers final: 3 residues processed: 34 average time/residue: 1.4227 time to fit residues: 49.3420 Evaluate side-chains 30 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.126588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.105874 restraints weight = 2198.274| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.59 r_work: 0.3041 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2195 Z= 0.193 Angle : 0.694 7.490 3026 Z= 0.351 Chirality : 0.048 0.154 369 Planarity : 0.004 0.030 358 Dihedral : 6.387 46.636 578 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.02 % Allowed : 12.06 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.53), residues: 243 helix: -1.99 (1.12), residues: 14 sheet: 1.02 (0.49), residues: 98 loop : -0.48 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 185 HIS 0.003 0.001 HIS A 110 PHE 0.016 0.002 PHE A 107 TYR 0.010 0.002 TYR A 215 ARG 0.004 0.001 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 7) link_NAG-ASN : angle 2.07651 ( 21) link_BETA1-4 : bond 0.00481 ( 6) link_BETA1-4 : angle 1.78119 ( 18) hydrogen bonds : bond 0.05532 ( 76) hydrogen bonds : angle 5.85025 ( 192) link_BETA1-6 : bond 0.00427 ( 2) link_BETA1-6 : angle 1.12351 ( 6) SS BOND : bond 0.00527 ( 3) SS BOND : angle 0.76474 ( 6) covalent geometry : bond 0.00440 ( 2177) covalent geometry : angle 0.66058 ( 2975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.236 Fit side-chains REVERT: A 231 TYR cc_start: 0.9317 (OUTLIER) cc_final: 0.8788 (p90) REVERT: A 237 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8608 (t80) outliers start: 8 outliers final: 4 residues processed: 33 average time/residue: 1.5601 time to fit residues: 52.4327 Evaluate side-chains 30 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 241 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.126826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106114 restraints weight = 2160.170| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.56 r_work: 0.3044 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2195 Z= 0.187 Angle : 0.692 7.661 3026 Z= 0.349 Chirality : 0.048 0.151 369 Planarity : 0.004 0.029 358 Dihedral : 6.421 46.766 578 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.52 % Allowed : 12.56 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.03 (0.53), residues: 243 helix: -2.08 (1.10), residues: 14 sheet: 1.01 (0.49), residues: 98 loop : -0.48 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 185 HIS 0.002 0.001 HIS A 110 PHE 0.016 0.002 PHE A 107 TYR 0.010 0.002 TYR A 215 ARG 0.003 0.001 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 7) link_NAG-ASN : angle 2.08416 ( 21) link_BETA1-4 : bond 0.00461 ( 6) link_BETA1-4 : angle 1.77832 ( 18) hydrogen bonds : bond 0.05493 ( 76) hydrogen bonds : angle 5.85394 ( 192) link_BETA1-6 : bond 0.00423 ( 2) link_BETA1-6 : angle 1.11231 ( 6) SS BOND : bond 0.00536 ( 3) SS BOND : angle 0.79499 ( 6) covalent geometry : bond 0.00425 ( 2177) covalent geometry : angle 0.65810 ( 2975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 486 Ramachandran restraints generated. 243 Oldfield, 0 Emsley, 243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.240 Fit side-chains REVERT: A 231 TYR cc_start: 0.9318 (OUTLIER) cc_final: 0.8721 (p90) REVERT: A 237 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8616 (t80) outliers start: 7 outliers final: 4 residues processed: 31 average time/residue: 1.4944 time to fit residues: 47.2390 Evaluate side-chains 30 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 241 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.106965 restraints weight = 2166.219| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.60 r_work: 0.3057 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2195 Z= 0.141 Angle : 0.633 7.124 3026 Z= 0.319 Chirality : 0.046 0.147 369 Planarity : 0.004 0.028 358 Dihedral : 6.186 46.501 578 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.52 % Allowed : 11.56 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.12 (0.54), residues: 243 helix: -1.82 (1.16), residues: 14 sheet: 1.04 (0.49), residues: 98 loop : -0.43 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 201 HIS 0.002 0.001 HIS A 110 PHE 0.016 0.002 PHE A 107 TYR 0.012 0.001 TYR A 215 ARG 0.003 0.001 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 7) link_NAG-ASN : angle 2.00682 ( 21) link_BETA1-4 : bond 0.00405 ( 6) link_BETA1-4 : angle 1.72073 ( 18) hydrogen bonds : bond 0.04966 ( 76) hydrogen bonds : angle 5.80330 ( 192) link_BETA1-6 : bond 0.00436 ( 2) link_BETA1-6 : angle 1.10086 ( 6) SS BOND : bond 0.00435 ( 3) SS BOND : angle 0.68123 ( 6) covalent geometry : bond 0.00312 ( 2177) covalent geometry : angle 0.59800 ( 2975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2718.23 seconds wall clock time: 47 minutes 11.60 seconds (2831.60 seconds total)