Starting phenix.real_space_refine on Sun Apr 5 01:29:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w04_65491/04_2026/9w04_65491_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w04_65491/04_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_65491/04_2026/9w04_65491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w04_65491/04_2026/9w04_65491.map" model { file = "/net/cci-nas-00/data/ceres_data/9w04_65491/04_2026/9w04_65491_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w04_65491/04_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/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: 1.67, per 1000 atoms: 0.24 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: 0.88 Conformation dependent library (CDL) restraints added in 201.9 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: 0.97 Time building geometry restraints manager: 1.04 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=" 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 bond pdb=" N ASP B 30 " pdb=" CA ASP B 30 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.17e-02 7.31e+03 8.56e+00 ... (remaining 7260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 9630 1.59 - 3.17: 480 3.17 - 4.76: 111 4.76 - 6.35: 20 6.35 - 7.93: 10 Bond angle restraints: 10251 Sorted by residual: 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=" CA ARG A 47 " pdb=" C ARG A 47 " pdb=" N VAL A 48 " ideal model delta sigma weight residual 115.36 121.72 -6.36 1.48e+00 4.57e-01 1.85e+01 angle pdb=" N ILE B 15 " pdb=" CA ILE B 15 " pdb=" C ILE B 15 " ideal model delta sigma weight residual 112.35 106.82 5.53 1.41e+00 5.03e-01 1.54e+01 angle pdb=" N ILE B 60 " pdb=" CA ILE B 60 " pdb=" C ILE B 60 " ideal model delta sigma weight residual 112.90 109.18 3.72 9.60e-01 1.09e+00 1.50e+01 angle pdb=" C THR A 50 " pdb=" N PRO A 51 " pdb=" CA PRO A 51 " ideal model delta sigma weight residual 119.05 123.26 -4.21 1.11e+00 8.12e-01 1.44e+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 - 0.122: 1119 0.122 - 0.243: 25 0.243 - 0.364: 0 0.364 - 0.486: 0 0.486 - 0.607: 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 2.35 -2.95 -0.61 2.00e-01 2.50e+01 9.22e+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 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.98e+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 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.57e+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: 2.350 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.780 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 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= 0.365 Angle : 0.847 7.933 10251 Z= 0.527 Chirality : 0.069 0.607 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 covalent geometry : bond 0.00615 ( 7265) covalent geometry : angle 0.84685 (10251) hydrogen bonds : bond 0.14480 ( 372) hydrogen bonds : angle 5.23319 ( 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 : 0.176 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: 0.4568 time to fit residues: 31.0709 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 : 0.219 ------------------------------------------------------------------------------- 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: 0.0370 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.095035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.075826 restraints weight = 13755.346| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.84 r_work: 0.3084 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7265 Z= 0.146 Angle : 0.569 7.968 10251 Z= 0.314 Chirality : 0.037 0.163 1154 Planarity : 0.004 0.035 969 Dihedral : 23.949 173.093 1891 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: 2.94 (0.33), residues: 605 helix: 3.05 (0.25), residues: 349 sheet: -1.06 (0.99), residues: 20 loop : 0.59 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 97 TYR 0.013 0.001 TYR A 95 PHE 0.008 0.001 PHE A 36 TRP 0.006 0.001 TRP B 309 HIS 0.006 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7265) covalent geometry : angle 0.56896 (10251) hydrogen bonds : bond 0.04227 ( 372) hydrogen bonds : angle 3.41087 ( 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 71 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.136 Fit side-chains REVERT: A 9 GLN cc_start: 0.8820 (tt0) cc_final: 0.8359 (tm-30) REVERT: A 170 SER cc_start: 0.9155 (m) cc_final: 0.8818 (m) outliers start: 9 outliers final: 3 residues processed: 70 average time/residue: 0.4093 time to fit residues: 30.6629 Evaluate side-chains 53 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 237 SER 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: 0.0000 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS A 195 ASN A 207 ASN B 12 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.093752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.074584 restraints weight = 13675.928| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.85 r_work: 0.3055 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7265 Z= 0.164 Angle : 0.550 7.659 10251 Z= 0.306 Chirality : 0.037 0.142 1154 Planarity : 0.004 0.037 969 Dihedral : 23.807 172.274 1889 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.53 % Allowed : 13.81 % Favored : 83.66 % 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: 3.11 (0.25), residues: 349 sheet: -0.96 (1.02), residues: 20 loop : 0.76 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 286 TYR 0.014 0.001 TYR A 95 PHE 0.007 0.001 PHE A 36 TRP 0.005 0.001 TRP B 309 HIS 0.005 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7265) covalent geometry : angle 0.54981 (10251) hydrogen bonds : bond 0.04276 ( 372) hydrogen bonds : angle 3.38500 ( 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 64 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.204 Fit side-chains REVERT: A 9 GLN cc_start: 0.8866 (tt0) cc_final: 0.8396 (tm-30) REVERT: A 170 SER cc_start: 0.9169 (m) cc_final: 0.8834 (m) outliers start: 13 outliers final: 6 residues processed: 63 average time/residue: 0.4569 time to fit residues: 30.6791 Evaluate side-chains 53 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 184 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3580 r_free = 0.3580 target = 0.094702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075473 restraints weight = 13860.165| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.85 r_work: 0.3079 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7265 Z= 0.144 Angle : 0.538 7.663 10251 Z= 0.297 Chirality : 0.036 0.152 1154 Planarity : 0.004 0.038 969 Dihedral : 23.778 174.921 1889 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 3.17 (0.33), residues: 605 helix: 3.15 (0.25), residues: 350 sheet: -0.47 (1.10), residues: 20 loop : 0.76 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.017 0.001 TYR A 95 PHE 0.008 0.001 PHE A 269 TRP 0.005 0.001 TRP B 309 HIS 0.004 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7265) covalent geometry : angle 0.53816 (10251) hydrogen bonds : bond 0.03978 ( 372) hydrogen bonds : angle 3.27211 ( 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 56 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.223 Fit side-chains REVERT: A 9 GLN cc_start: 0.8849 (tt0) cc_final: 0.8397 (tm-30) REVERT: A 170 SER cc_start: 0.9173 (m) cc_final: 0.8852 (m) REVERT: A 184 ASP cc_start: 0.8324 (t0) cc_final: 0.8102 (t0) outliers start: 9 outliers final: 6 residues processed: 55 average time/residue: 0.4663 time to fit residues: 27.3733 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 : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU 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: 4.9990 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.092906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073768 restraints weight = 13866.820| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.83 r_work: 0.3039 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7265 Z= 0.186 Angle : 0.553 7.553 10251 Z= 0.307 Chirality : 0.038 0.146 1154 Planarity : 0.004 0.036 969 Dihedral : 23.815 175.439 1889 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.56 % Allowed : 14.79 % Favored : 83.66 % 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: 3.07 (0.25), residues: 348 sheet: -0.41 (1.15), residues: 20 loop : 0.76 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 286 TYR 0.019 0.001 TYR A 95 PHE 0.008 0.002 PHE A 269 TRP 0.005 0.001 TRP B 309 HIS 0.006 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 7265) covalent geometry : angle 0.55266 (10251) hydrogen bonds : bond 0.04395 ( 372) hydrogen bonds : angle 3.41026 ( 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 55 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.205 Fit side-chains REVERT: A 9 GLN cc_start: 0.8874 (tt0) cc_final: 0.8414 (tm-30) REVERT: A 170 SER cc_start: 0.9190 (m) cc_final: 0.8860 (m) REVERT: A 184 ASP cc_start: 0.8484 (t0) cc_final: 0.8242 (OUTLIER) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.4643 time to fit residues: 26.7270 Evaluate side-chains 50 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 132 ILE 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: 0.7980 chunk 61 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.094572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.075652 restraints weight = 13859.071| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.84 r_work: 0.3083 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7265 Z= 0.144 Angle : 0.531 8.284 10251 Z= 0.294 Chirality : 0.036 0.148 1154 Planarity : 0.004 0.037 969 Dihedral : 23.809 176.954 1889 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.75 % Allowed : 14.79 % 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: 3.23 (0.33), residues: 605 helix: 3.15 (0.25), residues: 349 sheet: -0.23 (1.19), 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 0.019 0.001 TYR A 95 PHE 0.010 0.001 PHE A 269 TRP 0.005 0.001 TRP B 309 HIS 0.004 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 7265) covalent geometry : angle 0.53060 (10251) hydrogen bonds : bond 0.03956 ( 372) hydrogen bonds : angle 3.25949 ( 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 59 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.215 Fit side-chains REVERT: A 9 GLN cc_start: 0.8838 (tt0) cc_final: 0.8386 (tm-30) REVERT: A 170 SER cc_start: 0.9167 (m) cc_final: 0.8837 (m) REVERT: A 184 ASP cc_start: 0.8467 (t0) cc_final: 0.8235 (OUTLIER) outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 0.4453 time to fit residues: 27.5166 Evaluate side-chains 52 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 132 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.092321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.073399 restraints weight = 13792.330| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.83 r_work: 0.3038 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7265 Z= 0.203 Angle : 0.577 7.796 10251 Z= 0.316 Chirality : 0.039 0.149 1154 Planarity : 0.004 0.035 969 Dihedral : 23.849 178.184 1889 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.95 % Allowed : 14.98 % Favored : 83.07 % 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: 3.14 (0.33), residues: 605 helix: 3.04 (0.25), residues: 348 sheet: -0.16 (1.19), residues: 20 loop : 0.92 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 286 TYR 0.023 0.001 TYR A 95 PHE 0.010 0.002 PHE A 269 TRP 0.005 0.001 TRP B 309 HIS 0.007 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 7265) covalent geometry : angle 0.57653 (10251) hydrogen bonds : bond 0.04520 ( 372) hydrogen bonds : angle 3.47005 ( 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 58 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.388 Fit side-chains REVERT: A 9 GLN cc_start: 0.8818 (tt0) cc_final: 0.8385 (tm-30) REVERT: A 170 SER cc_start: 0.9183 (m) cc_final: 0.8853 (m) REVERT: A 184 ASP cc_start: 0.8559 (t0) cc_final: 0.8316 (OUTLIER) outliers start: 10 outliers final: 7 residues processed: 57 average time/residue: 0.4653 time to fit residues: 28.2331 Evaluate side-chains 53 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 237 SER 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: 0.0770 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.095398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.076477 restraints weight = 13951.631| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.85 r_work: 0.3102 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7265 Z= 0.132 Angle : 0.534 8.878 10251 Z= 0.293 Chirality : 0.035 0.147 1154 Planarity : 0.004 0.037 969 Dihedral : 23.721 178.606 1889 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.36 % Allowed : 15.95 % Favored : 82.68 % 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: 3.28 (0.33), residues: 605 helix: 3.08 (0.25), residues: 351 sheet: -0.04 (1.19), residues: 20 loop : 1.07 (0.43), residues: 234 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 0.010 0.001 PHE A 269 TRP 0.006 0.001 TRP B 309 HIS 0.004 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7265) covalent geometry : angle 0.53411 (10251) hydrogen bonds : bond 0.03841 ( 372) hydrogen bonds : angle 3.22546 ( 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 60 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.224 Fit side-chains REVERT: A 9 GLN cc_start: 0.8819 (tt0) cc_final: 0.8370 (tm-30) REVERT: A 170 SER cc_start: 0.9159 (m) cc_final: 0.8824 (m) REVERT: A 184 ASP cc_start: 0.8463 (t0) cc_final: 0.8235 (OUTLIER) outliers start: 7 outliers final: 8 residues processed: 58 average time/residue: 0.4356 time to fit residues: 27.0336 Evaluate side-chains 58 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU 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 A residue 299 ILE 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: 0.9990 chunk 36 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.094919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.075964 restraints weight = 13853.316| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.84 r_work: 0.3090 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7265 Z= 0.145 Angle : 0.552 9.032 10251 Z= 0.301 Chirality : 0.036 0.145 1154 Planarity : 0.004 0.036 969 Dihedral : 23.731 178.482 1889 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.56 % Allowed : 15.95 % Favored : 82.49 % 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: 3.31 (0.33), residues: 605 helix: 3.08 (0.25), residues: 351 sheet: -0.09 (1.18), residues: 20 loop : 1.14 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 286 TYR 0.025 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 54 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7265) covalent geometry : angle 0.55151 (10251) hydrogen bonds : bond 0.03926 ( 372) hydrogen bonds : angle 3.23764 ( 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 58 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.187 Fit side-chains REVERT: A 9 GLN cc_start: 0.8813 (tt0) cc_final: 0.8360 (tm-30) REVERT: A 170 SER cc_start: 0.9198 (m) cc_final: 0.8903 (m) REVERT: A 184 ASP cc_start: 0.8508 (t0) cc_final: 0.8293 (OUTLIER) outliers start: 8 outliers final: 7 residues processed: 56 average time/residue: 0.4533 time to fit residues: 27.0273 Evaluate side-chains 54 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU 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: 1.9990 chunk 59 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 18 optimal weight: 0.0870 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.097090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.078128 restraints weight = 13788.776| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.82 r_work: 0.3133 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7265 Z= 0.125 Angle : 0.531 10.118 10251 Z= 0.289 Chirality : 0.035 0.143 1154 Planarity : 0.003 0.036 969 Dihedral : 23.739 179.765 1889 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.36 % Allowed : 16.15 % Favored : 82.49 % 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: 3.41 (0.33), residues: 605 helix: 3.13 (0.25), residues: 351 sheet: 0.00 (1.16), residues: 20 loop : 1.21 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 286 TYR 0.026 0.001 TYR A 95 PHE 0.009 0.001 PHE A 269 TRP 0.006 0.001 TRP B 309 HIS 0.004 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7265) covalent geometry : angle 0.53144 (10251) hydrogen bonds : bond 0.03683 ( 372) hydrogen bonds : angle 3.13545 ( 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 61 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.209 Fit side-chains REVERT: A 9 GLN cc_start: 0.8808 (tt0) cc_final: 0.8354 (tm-30) REVERT: A 170 SER cc_start: 0.9173 (m) cc_final: 0.8887 (m) outliers start: 7 outliers final: 8 residues processed: 59 average time/residue: 0.4679 time to fit residues: 29.3896 Evaluate side-chains 56 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 299 ILE 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: 0.8980 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 0.0060 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.096656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.077710 restraints weight = 13719.270| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.83 r_work: 0.3123 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7265 Z= 0.131 Angle : 0.533 10.394 10251 Z= 0.290 Chirality : 0.035 0.142 1154 Planarity : 0.004 0.036 969 Dihedral : 23.747 179.594 1889 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: 3.26 (0.33), residues: 605 helix: 2.96 (0.25), residues: 358 sheet: 0.14 (1.21), residues: 20 loop : 1.15 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 213 TYR 0.026 0.001 TYR A 95 PHE 0.008 0.001 PHE A 36 TRP 0.005 0.001 TRP B 309 HIS 0.004 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7265) covalent geometry : angle 0.53297 (10251) hydrogen bonds : bond 0.03736 ( 372) hydrogen bonds : angle 3.15778 ( 989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2413.75 seconds wall clock time: 41 minutes 54.04 seconds (2514.04 seconds total)