Starting phenix.real_space_refine on Tue Aug 4 21:53:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w04_65491/08_2026/9w04_65491_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w04_65491/08_2026/9w04_65491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w04_65491/08_2026/9w04_65491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w04_65491/08_2026/9w04_65491.map" model { file = "/net/cci-nas-00/data/ceres_data/9w04_65491/08_2026/9w04_65491_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w04_65491/08_2026/9w04_65491_neut.cif" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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: 6 Type Number sf(0) Gaussians P 98 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 3994 2.51 5 N 1287 2.21 5 O 1516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6927 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2412 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 12, 'TRANS': 289} Chain breaks: 1 Chain: "B" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2468 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 12, 'TRANS': 296} Chain: "C" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 774 Classifications: {'DNA': 1, 'RNA': 36} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 14, 'rna3p': 22} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "E" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 242 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "F" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 374 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "G" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 266 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.77, per 1000 atoms: 0.26 Number of scatterers: 6927 At special positions: 0 Unit cell: (86.275, 74.675, 97.875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 98 15.00 Mg 2 11.99 O 1516 8.00 N 1287 7.00 C 3994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 305.5 milliseconds 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 65.1% alpha, 4.6% beta 33 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 50 through 59 Processing helix chain 'A' and resid 65 through 97 Processing helix chain 'A' and resid 103 through 134 Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.501A pdb=" N VAL A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.600A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.583A pdb=" N ARG A 185 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 210 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 253 through 282 removed outlier: 3.685A pdb=" N ARG A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.119A pdb=" N GLY A 306 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 50 through 59 Processing helix chain 'B' and resid 65 through 97 Processing helix chain 'B' and resid 103 through 134 Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.504A pdb=" N GLN B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.676A pdb=" N VAL B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.944A pdb=" N ARG B 185 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 212 removed outlier: 4.032A pdb=" N LYS B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 230 removed outlier: 3.780A pdb=" N VAL B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 253 through 281 removed outlier: 3.646A pdb=" N ARG B 257 " --> pdb=" O LYS B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 301 through 305 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 238 Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AA4, first strand: chain 'B' and resid 234 through 238 291 hydrogen bonds defined for protein. 831 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1739 1.33 - 1.45: 1794 1.45 - 1.57: 3486 1.57 - 1.69: 192 1.69 - 1.81: 54 Bond restraints: 7265 Sorted by residual: bond pdb=" C THR A 46 " pdb=" N ARG A 47 " ideal model delta sigma weight residual 1.331 1.266 0.065 1.22e-02 6.72e+03 2.88e+01 bond pdb=" N VAL A 48 " pdb=" CA VAL A 48 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.14e-02 7.69e+03 1.25e+01 bond pdb=" C ARG A 47 " pdb=" N VAL A 48 " ideal model delta sigma weight residual 1.331 1.284 0.047 1.40e-02 5.10e+03 1.12e+01 bond pdb=" C3' DA D 6 " pdb=" O3' DA D 6 " ideal model delta sigma weight residual 1.435 1.477 -0.042 1.30e-02 5.92e+03 1.06e+01 bond pdb=" N VAL B 48 " pdb=" CA VAL B 48 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.20e-02 6.94e+03 9.14e+00 ... (remaining 7260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 9499 1.59 - 3.17: 593 3.17 - 4.76: 127 4.76 - 6.35: 22 6.35 - 7.93: 10 Bond angle restraints: 10251 Sorted by residual: angle pdb=" O4' C C 8 " pdb=" C1' C C 8 " pdb=" N1 C C 8 " ideal model delta sigma weight residual 108.20 112.55 -4.35 8.00e-01 1.56e+00 2.96e+01 angle pdb=" CA THR A 46 " pdb=" C THR A 46 " pdb=" N ARG A 47 " ideal model delta sigma weight residual 115.27 121.90 -6.63 1.24e+00 6.50e-01 2.86e+01 angle pdb=" O4' DG D 7 " pdb=" C4' DG D 7 " pdb=" C3' DG D 7 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" C3' G C 36 " pdb=" C2' G C 36 " pdb=" C1' G C 36 " ideal model delta sigma weight residual 101.50 97.96 3.54 8.00e-01 1.56e+00 1.95e+01 angle pdb=" N3 DT F 7 " pdb=" C4 DT F 7 " pdb=" O4 DT F 7 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 10246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 3903 35.11 - 70.21: 327 70.21 - 105.32: 16 105.32 - 140.43: 2 140.43 - 175.54: 7 Dihedral angle restraints: 4255 sinusoidal: 2489 harmonic: 1766 Sorted by residual: dihedral pdb=" C4' DT D 12 " pdb=" C3' DT D 12 " pdb=" O3' DT D 12 " pdb=" P DT D 13 " ideal model delta sinusoidal sigma weight residual 220.00 44.46 175.54 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA D 6 " pdb=" C3' DA D 6 " pdb=" O3' DA D 6 " pdb=" P DG D 7 " ideal model delta sinusoidal sigma weight residual -140.00 29.97 -169.97 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA F 8 " pdb=" C3' DA F 8 " pdb=" O3' DA F 8 " pdb=" P DA F 9 " ideal model delta sinusoidal sigma weight residual 220.00 50.27 169.73 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 4252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1076 0.124 - 0.247: 68 0.247 - 0.371: 0 0.371 - 0.494: 0 0.494 - 0.618: 10 Chirality restraints: 1154 Sorted by residual: chirality pdb=" P DT G 29 " pdb=" OP1 DT G 29 " pdb=" OP2 DT G 29 " pdb=" O5' DT G 29 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.62 2.00e-01 2.50e+01 9.54e+00 chirality pdb=" P DT G 34 " pdb=" OP1 DT G 34 " pdb=" OP2 DT G 34 " pdb=" O5' DT G 34 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" P DC G 32 " pdb=" OP1 DC G 32 " pdb=" OP2 DC G 32 " pdb=" O5' DC G 32 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.56 2.00e-01 2.50e+01 7.86e+00 ... (remaining 1151 not shown) Planarity restraints: 969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 8 " -0.046 2.00e-02 2.50e+03 2.40e-02 1.30e+01 pdb=" N1 C C 8 " 0.052 2.00e-02 2.50e+03 pdb=" C2 C C 8 " 0.006 2.00e-02 2.50e+03 pdb=" O2 C C 8 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C C 8 " -0.006 2.00e-02 2.50e+03 pdb=" C4 C C 8 " -0.007 2.00e-02 2.50e+03 pdb=" N4 C C 8 " -0.011 2.00e-02 2.50e+03 pdb=" C5 C C 8 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C C 8 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 52 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C ARG A 52 " 0.049 2.00e-02 2.50e+03 pdb=" O ARG A 52 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA A 53 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 46 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.41e+00 pdb=" C THR A 46 " -0.044 2.00e-02 2.50e+03 pdb=" O THR A 46 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 47 " 0.016 2.00e-02 2.50e+03 ... (remaining 966 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 7 2.27 - 2.93: 2875 2.93 - 3.59: 10876 3.59 - 4.24: 18716 4.24 - 4.90: 28788 Nonbonded interactions: 61262 Sorted by model distance: nonbonded pdb=" O3' DA F 22 " pdb="MG MG F 101 " model vdw 1.618 2.170 nonbonded pdb=" O3' DT D 22 " pdb="MG MG B 401 " model vdw 1.932 2.170 nonbonded pdb=" NE2 HIS A 58 " pdb="MG MG F 101 " model vdw 1.970 2.250 nonbonded pdb=" OD1 ASP B 30 " pdb="MG MG B 401 " model vdw 2.042 2.170 nonbonded pdb=" OD1 ASP A 30 " pdb="MG MG F 101 " model vdw 2.062 2.170 ... (remaining 61257 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 'A' selection = (chain 'B' and (resid 1 through 290 or resid 298 through 309)) } 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: 1.950 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.900 Find NCS groups from input model: 0.090 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:8.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 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 : 0.006 0.065 7265 Z= 0.490 Angle : 0.902 7.933 10251 Z= 0.656 Chirality : 0.076 0.618 1154 Planarity : 0.005 0.071 969 Dihedral : 22.078 175.535 3115 Min Nonbonded Distance : 1.618 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.58 % Allowed : 13.23 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.33), residues: 605 helix: 2.35 (0.26), residues: 347 sheet: -1.94 (0.91), residues: 20 loop : 0.24 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 97 TYR 0.011 0.001 TYR A 273 PHE 0.007 0.002 PHE B 36 TRP 0.004 0.001 TRP B 309 HIS 0.008 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.49 ( 7265) covalent geometry : angle 0.90177 / 0.66 (10251) hydrogen bonds : bond 0.14480 / 9.47 ( 372) hydrogen bonds : angle 5.23319 / 3.72 ( 989) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.225 Fit side-chains REVERT: A 9 GLN cc_start: 0.8769 (tt0) cc_final: 0.8528 (tm-30) REVERT: A 88 MET cc_start: 0.9426 (tpp) cc_final: 0.9209 (mmm) REVERT: A 170 SER cc_start: 0.9197 (m) cc_final: 0.8885 (m) REVERT: B 60 ILE cc_start: 0.7961 (mm) cc_final: 0.7648 (pt) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 0.5047 time to fit residues: 34.4367 Evaluate side-chains 53 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.0570 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN B 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.093903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.074790 restraints weight = 13713.945| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.81 r_work: 0.3062 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7265 Z= 0.149 Angle : 0.636 9.212 10251 Z= 0.359 Chirality : 0.047 0.339 1154 Planarity : 0.004 0.040 969 Dihedral : 24.221 172.325 1891 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.75 % Allowed : 14.01 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.33), residues: 605 helix: 2.88 (0.26), residues: 346 sheet: -1.15 (0.99), residues: 20 loop : 0.45 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 286 TYR 0.014 0.002 TYR A 95 PHE 0.007 0.001 PHE A 269 TRP 0.006 0.001 TRP B 309 HIS 0.005 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 ( 7265) covalent geometry : angle 0.63562 / 0.36 (10251) hydrogen bonds : bond 0.05312 / 3.57 ( 372) hydrogen bonds : angle 3.77807 / 2.66 ( 989) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.218 Fit side-chains REVERT: A 9 GLN cc_start: 0.8866 (tt0) cc_final: 0.8424 (tm-30) REVERT: A 170 SER cc_start: 0.9109 (m) cc_final: 0.8801 (m) REVERT: A 285 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8808 (t) REVERT: B 32 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7864 (mp) outliers start: 9 outliers final: 5 residues processed: 65 average time/residue: 0.3946 time to fit residues: 27.5187 Evaluate side-chains 55 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.0040 chunk 54 optimal weight: 0.6980 chunk 65 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 204 ASN B 12 HIS B 204 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.094570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.075316 restraints weight = 13530.054| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.81 r_work: 0.3069 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7265 Z= 0.135 Angle : 0.599 8.964 10251 Z= 0.336 Chirality : 0.045 0.350 1154 Planarity : 0.004 0.045 969 Dihedral : 24.049 173.575 1889 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.33 % Allowed : 13.62 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.33), residues: 605 helix: 3.10 (0.25), residues: 345 sheet: -0.59 (1.07), residues: 20 loop : 0.43 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 64 TYR 0.016 0.001 TYR A 95 PHE 0.008 0.001 PHE A 269 TRP 0.005 0.001 TRP B 309 HIS 0.005 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.13 ( 7265) covalent geometry : angle 0.59926 / 0.34 (10251) hydrogen bonds : bond 0.04716 / 3.16 ( 372) hydrogen bonds : angle 3.54846 / 2.50 ( 989) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.226 Fit side-chains REVERT: A 9 GLN cc_start: 0.8829 (tt0) cc_final: 0.8356 (tm-30) REVERT: A 170 SER cc_start: 0.9106 (m) cc_final: 0.8784 (m) REVERT: A 184 ASP cc_start: 0.8054 (t0) cc_final: 0.7646 (t0) outliers start: 12 outliers final: 4 residues processed: 65 average time/residue: 0.4147 time to fit residues: 28.9996 Evaluate side-chains 54 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 29 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN B 12 HIS B 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.095039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.075700 restraints weight = 13748.465| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.84 r_work: 0.3077 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7265 Z= 0.133 Angle : 0.583 9.100 10251 Z= 0.327 Chirality : 0.045 0.352 1154 Planarity : 0.004 0.041 969 Dihedral : 23.899 174.065 1889 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.95 % Allowed : 13.23 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.33), residues: 605 helix: 3.14 (0.25), residues: 349 sheet: -0.03 (1.16), residues: 20 loop : 0.59 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 286 TYR 0.018 0.001 TYR A 95 PHE 0.008 0.001 PHE A 269 TRP 0.005 0.001 TRP B 274 HIS 0.005 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 ( 7265) covalent geometry : angle 0.58342 / 0.33 (10251) hydrogen bonds : bond 0.04367 / 2.92 ( 372) hydrogen bonds : angle 3.36342 / 2.36 ( 989) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.198 Fit side-chains REVERT: A 9 GLN cc_start: 0.8826 (tt0) cc_final: 0.8370 (tm-30) REVERT: A 170 SER cc_start: 0.9073 (m) cc_final: 0.8740 (m) REVERT: A 184 ASP cc_start: 0.8121 (t0) cc_final: 0.7684 (t0) outliers start: 10 outliers final: 5 residues processed: 64 average time/residue: 0.4118 time to fit residues: 28.3109 Evaluate side-chains 55 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 58 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 207 ASN B 12 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.094631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.075291 restraints weight = 13780.905| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.85 r_work: 0.3069 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7265 Z= 0.140 Angle : 0.582 9.103 10251 Z= 0.325 Chirality : 0.045 0.354 1154 Planarity : 0.004 0.039 969 Dihedral : 23.849 174.251 1889 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.36 % Allowed : 14.40 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.09 (0.33), residues: 605 helix: 3.09 (0.25), residues: 349 sheet: -0.06 (1.15), residues: 20 loop : 0.70 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 286 TYR 0.018 0.001 TYR A 95 PHE 0.009 0.001 PHE A 269 TRP 0.005 0.001 TRP B 274 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 ( 7265) covalent geometry : angle 0.58248 / 0.33 (10251) hydrogen bonds : bond 0.04386 / 2.93 ( 372) hydrogen bonds : angle 3.34802 / 2.35 ( 989) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.140 Fit side-chains REVERT: A 9 GLN cc_start: 0.8806 (tt0) cc_final: 0.8334 (tm-30) REVERT: A 170 SER cc_start: 0.9102 (m) cc_final: 0.8767 (m) REVERT: A 184 ASP cc_start: 0.8289 (t0) cc_final: 0.7875 (t0) outliers start: 7 outliers final: 5 residues processed: 58 average time/residue: 0.4277 time to fit residues: 26.4353 Evaluate side-chains 54 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 46 optimal weight: 0.4980 chunk 33 optimal weight: 0.0770 chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN B 12 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.094514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.075069 restraints weight = 13784.737| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.85 r_work: 0.3069 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7265 Z= 0.143 Angle : 0.575 9.125 10251 Z= 0.323 Chirality : 0.045 0.357 1154 Planarity : 0.004 0.038 969 Dihedral : 23.835 174.704 1889 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.33 % Allowed : 13.62 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.10 (0.33), residues: 605 helix: 3.05 (0.25), residues: 349 sheet: 0.05 (1.19), residues: 20 loop : 0.77 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 286 TYR 0.019 0.001 TYR A 95 PHE 0.007 0.001 PHE A 269 TRP 0.005 0.001 TRP B 274 HIS 0.007 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 ( 7265) covalent geometry : angle 0.57534 / 0.32 (10251) hydrogen bonds : bond 0.04333 / 2.90 ( 372) hydrogen bonds : angle 3.33469 / 2.34 ( 989) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.162 Fit side-chains REVERT: A 9 GLN cc_start: 0.8811 (tt0) cc_final: 0.8366 (tm-30) REVERT: A 170 SER cc_start: 0.9127 (m) cc_final: 0.8784 (m) REVERT: A 184 ASP cc_start: 0.8380 (t0) cc_final: 0.7976 (t0) outliers start: 12 outliers final: 7 residues processed: 60 average time/residue: 0.4334 time to fit residues: 27.8157 Evaluate side-chains 55 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 HIS A 204 ASN B 12 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.092701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073358 restraints weight = 13757.787| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.83 r_work: 0.3033 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7265 Z= 0.194 Angle : 0.609 9.148 10251 Z= 0.338 Chirality : 0.047 0.367 1154 Planarity : 0.004 0.037 969 Dihedral : 23.828 174.537 1889 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.75 % Allowed : 14.40 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.33), residues: 605 helix: 2.99 (0.25), residues: 347 sheet: -0.05 (1.13), residues: 20 loop : 0.79 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 286 TYR 0.022 0.001 TYR A 95 PHE 0.009 0.002 PHE A 269 TRP 0.006 0.001 TRP B 309 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 ( 7265) covalent geometry : angle 0.60865 / 0.34 (10251) hydrogen bonds : bond 0.04826 / 3.22 ( 372) hydrogen bonds : angle 3.44924 / 2.42 ( 989) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.223 Fit side-chains REVERT: A 9 GLN cc_start: 0.8834 (tt0) cc_final: 0.8390 (tm-30) REVERT: A 170 SER cc_start: 0.9153 (m) cc_final: 0.8828 (m) REVERT: A 184 ASP cc_start: 0.8526 (t0) cc_final: 0.8151 (t0) outliers start: 9 outliers final: 6 residues processed: 55 average time/residue: 0.4166 time to fit residues: 24.5013 Evaluate side-chains 51 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN B 12 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.094284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.074870 restraints weight = 13890.041| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.86 r_work: 0.3065 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7265 Z= 0.132 Angle : 0.569 9.095 10251 Z= 0.321 Chirality : 0.045 0.369 1154 Planarity : 0.004 0.038 969 Dihedral : 23.850 176.120 1889 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.95 % Allowed : 14.59 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.33), residues: 605 helix: 3.02 (0.25), residues: 349 sheet: 0.12 (1.14), residues: 20 loop : 0.88 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 286 TYR 0.022 0.001 TYR A 95 PHE 0.010 0.001 PHE A 269 TRP 0.005 0.001 TRP B 274 HIS 0.005 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.13 ( 7265) covalent geometry : angle 0.56854 / 0.32 (10251) hydrogen bonds : bond 0.04287 / 2.88 ( 372) hydrogen bonds : angle 3.36369 / 2.36 ( 989) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.152 Fit side-chains REVERT: A 9 GLN cc_start: 0.8820 (tt0) cc_final: 0.8375 (tm-30) REVERT: A 170 SER cc_start: 0.9117 (m) cc_final: 0.8775 (m) REVERT: A 184 ASP cc_start: 0.8457 (t0) cc_final: 0.8081 (t0) outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.4019 time to fit residues: 24.1145 Evaluate side-chains 54 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN B 12 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.095279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.075897 restraints weight = 13765.771| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.86 r_work: 0.3084 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7265 Z= 0.131 Angle : 0.557 8.784 10251 Z= 0.314 Chirality : 0.044 0.369 1154 Planarity : 0.004 0.038 969 Dihedral : 23.806 178.090 1889 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.95 % Allowed : 14.79 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.33), residues: 605 helix: 3.05 (0.25), residues: 349 sheet: 0.07 (1.13), residues: 20 loop : 0.99 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 286 TYR 0.022 0.001 TYR A 95 PHE 0.009 0.001 PHE A 269 TRP 0.006 0.001 TRP B 274 HIS 0.004 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 ( 7265) covalent geometry : angle 0.55691 / 0.31 (10251) hydrogen bonds : bond 0.04092 / 2.74 ( 372) hydrogen bonds : angle 3.26340 / 2.29 ( 989) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.293 Fit side-chains REVERT: A 9 GLN cc_start: 0.8815 (tt0) cc_final: 0.8364 (tm-30) REVERT: A 170 SER cc_start: 0.9109 (m) cc_final: 0.8764 (m) REVERT: A 184 ASP cc_start: 0.8483 (t0) cc_final: 0.8156 (t0) outliers start: 10 outliers final: 6 residues processed: 58 average time/residue: 0.4272 time to fit residues: 26.5314 Evaluate side-chains 52 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 16 optimal weight: 0.0980 chunk 59 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 29 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.096568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.077360 restraints weight = 13734.661| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.86 r_work: 0.3111 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7265 Z= 0.121 Angle : 0.573 8.541 10251 Z= 0.320 Chirality : 0.043 0.371 1154 Planarity : 0.004 0.038 969 Dihedral : 23.834 179.547 1889 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.17 % Allowed : 16.73 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.33), residues: 605 helix: 3.12 (0.25), residues: 349 sheet: 0.05 (1.14), residues: 20 loop : 1.02 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 286 TYR 0.024 0.001 TYR A 95 PHE 0.009 0.001 PHE A 269 TRP 0.010 0.001 TRP A 307 HIS 0.007 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.12 ( 7265) covalent geometry : angle 0.57260 / 0.32 (10251) hydrogen bonds : bond 0.03937 / 2.64 ( 372) hydrogen bonds : angle 3.21767 / 2.26 ( 989) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.245 Fit side-chains REVERT: A 9 GLN cc_start: 0.8804 (tt0) cc_final: 0.8354 (tm-30) REVERT: A 170 SER cc_start: 0.9104 (m) cc_final: 0.8786 (m) REVERT: A 184 ASP cc_start: 0.8449 (t0) cc_final: 0.8122 (t0) outliers start: 6 outliers final: 5 residues processed: 58 average time/residue: 0.4243 time to fit residues: 26.3082 Evaluate side-chains 53 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 0.0050 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.094849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.075414 restraints weight = 13625.647| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.84 r_work: 0.3078 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7265 Z= 0.149 Angle : 0.575 8.161 10251 Z= 0.320 Chirality : 0.045 0.375 1154 Planarity : 0.004 0.044 969 Dihedral : 23.817 179.368 1889 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.36 % Allowed : 16.73 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.26 (0.33), residues: 605 helix: 3.08 (0.25), residues: 349 sheet: 0.00 (1.14), residues: 20 loop : 1.04 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 286 TYR 0.026 0.001 TYR A 95 PHE 0.009 0.002 PHE A 269 TRP 0.005 0.001 TRP B 274 HIS 0.006 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 ( 7265) covalent geometry : angle 0.57505 / 0.32 (10251) hydrogen bonds : bond 0.04230 / 2.83 ( 372) hydrogen bonds : angle 3.26518 / 2.29 ( 989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2246.10 seconds wall clock time: 38 minutes 55.12 seconds (2335.12 seconds total)