Starting phenix.real_space_refine on Thu Jul 2 02:09:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21kl_67763/07_2026/21kl_67763_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/21kl_67763/07_2026/21kl_67763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21kl_67763/07_2026/21kl_67763_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21kl_67763/07_2026/21kl_67763_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21kl_67763/07_2026/21kl_67763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21kl_67763/07_2026/21kl_67763.map" } resolution = 3.19 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= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 94 5.49 5 S 24 5.16 5 C 3257 2.51 5 N 1055 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5706 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1897 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1851 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 1 Chain: "C" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 728 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 12, 'rna3p': 21} Chain: "D" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 610 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "E" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 620 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Time building chain proxies: 1.31, per 1000 atoms: 0.23 Number of scatterers: 5706 At special positions: 0 Unit cell: (59.45, 74.675, 100.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 94 15.00 O 1276 8.00 N 1055 7.00 C 3257 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: 0.50 Conformation dependent library (CDL) restraints added in 137.9 milliseconds 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 878 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 2 sheets defined 72.6% alpha, 3.4% beta 29 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 66 through 97 removed outlier: 4.089A pdb=" N GLU A 70 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 71 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET A 88 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 134 Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.766A pdb=" N GLN A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 168 through 177 removed outlier: 4.165A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TRP A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 195 through 210 Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.599A pdb=" N VAL A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'B' and resid 67 through 97 Processing helix chain 'B' and resid 103 through 134 removed outlier: 3.577A pdb=" N HIS B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.748A pdb=" N VAL B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.529A pdb=" N VAL B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 167 through 177 removed outlier: 3.529A pdb=" N ALA B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 195 through 212 removed outlier: 3.963A pdb=" N LYS B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 231 removed outlier: 3.953A 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 282 removed outlier: 3.649A pdb=" N ARG B 257 " --> pdb=" O LYS B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.987A pdb=" N GLY B 306 " --> pdb=" O GLN B 303 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 238 Processing sheet with id=AA2, first strand: chain 'B' and resid 234 through 238 247 hydrogen bonds defined for protein. 717 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.59 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: 1319 1.33 - 1.45: 1650 1.45 - 1.57: 2817 1.57 - 1.69: 185 1.69 - 1.81: 44 Bond restraints: 6015 Sorted by residual: bond pdb=" C1' DC D 14 " pdb=" N1 DC D 14 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 1.00e+01 bond pdb=" C3' DG D 8 " pdb=" C2' DG D 8 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.14e+00 bond pdb=" C1' DT D 12 " pdb=" N1 DT D 12 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.71e+00 bond pdb=" C3' DA E 17 " pdb=" C2' DA E 17 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.11e+00 bond pdb=" C1' DC E 32 " pdb=" N1 DC E 32 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.59e+00 ... (remaining 6010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 8088 1.52 - 3.05: 361 3.05 - 4.57: 66 4.57 - 6.10: 24 6.10 - 7.62: 2 Bond angle restraints: 8541 Sorted by residual: angle pdb=" O4' DG D 21 " pdb=" C4' DG D 21 " pdb=" C3' DG D 21 " ideal model delta sigma weight residual 106.00 102.64 3.36 6.00e-01 2.78e+00 3.13e+01 angle pdb=" N3 DT E 28 " pdb=" C4 DT E 28 " pdb=" O4 DT E 28 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT D 28 " pdb=" C4 DT D 28 " pdb=" O4 DT D 28 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT D 30 " pdb=" C4 DT D 30 " pdb=" O4 DT D 30 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" O4' DT D 24 " pdb=" C4' DT D 24 " pdb=" C3' DT D 24 " ideal model delta sigma weight residual 106.00 103.50 2.50 6.00e-01 2.78e+00 1.74e+01 ... (remaining 8536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.64: 3165 34.64 - 69.28: 298 69.28 - 103.91: 19 103.91 - 138.55: 2 138.55 - 173.19: 8 Dihedral angle restraints: 3492 sinusoidal: 2135 harmonic: 1357 Sorted by residual: 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 220.00 46.81 173.19 1 3.50e+01 8.16e-04 1.56e+01 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 48.67 171.33 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC E 12 " pdb=" C3' DC E 12 " pdb=" O3' DC E 12 " pdb=" P DG E 13 " ideal model delta sinusoidal sigma weight residual 220.00 49.21 170.79 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 3489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 908 0.112 - 0.225: 44 0.225 - 0.337: 0 0.337 - 0.450: 0 0.450 - 0.562: 10 Chirality restraints: 962 Sorted by residual: chirality pdb=" P DG D 21 " pdb=" OP1 DG D 21 " pdb=" OP2 DG D 21 " pdb=" O5' DG D 21 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" P DT E 20 " pdb=" OP1 DT E 20 " pdb=" OP2 DT E 20 " pdb=" O5' DT E 20 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.56 2.00e-01 2.50e+01 7.84e+00 chirality pdb=" P DA E 21 " pdb=" OP1 DA E 21 " pdb=" OP2 DA E 21 " pdb=" O5' DA E 21 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.54 2.00e-01 2.50e+01 7.16e+00 ... (remaining 959 not shown) Planarity restraints: 754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 8 " -0.034 2.00e-02 2.50e+03 1.80e-02 7.29e+00 pdb=" N1 C C 8 " 0.040 2.00e-02 2.50e+03 pdb=" C2 C C 8 " 0.005 2.00e-02 2.50e+03 pdb=" O2 C C 8 " 0.002 2.00e-02 2.50e+03 pdb=" N3 C C 8 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C C 8 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C C 8 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C C 8 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C C 8 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 184 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" CG ASP A 184 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP A 184 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP A 184 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 7 " 0.021 2.00e-02 2.50e+03 1.14e-02 2.92e+00 pdb=" N1 U C 7 " -0.026 2.00e-02 2.50e+03 pdb=" C2 U C 7 " -0.000 2.00e-02 2.50e+03 pdb=" O2 U C 7 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U C 7 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U C 7 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U C 7 " 0.006 2.00e-02 2.50e+03 pdb=" C5 U C 7 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U C 7 " -0.003 2.00e-02 2.50e+03 ... (remaining 751 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 252 2.70 - 3.25: 5513 3.25 - 3.80: 10322 3.80 - 4.35: 13078 4.35 - 4.90: 20055 Nonbonded interactions: 49220 Sorted by model distance: nonbonded pdb=" O LYS A 167 " pdb=" NZ LYS A 167 " model vdw 2.152 3.120 nonbonded pdb=" O ASP A 184 " pdb=" OD1 ASP A 184 " model vdw 2.170 3.040 nonbonded pdb=" N GLU A 70 " pdb=" OE1 GLU A 70 " model vdw 2.240 3.120 nonbonded pdb=" N GLU B 304 " pdb=" OE1 GLU B 304 " model vdw 2.250 3.120 nonbonded pdb=" OG SER A 170 " pdb=" OP2 C C 18 " model vdw 2.251 3.040 ... (remaining 49215 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' and (resid 66 through 286 or resid 300 through 309)) selection = chain 'B' } 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.240 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 : 0.005 0.044 6015 Z= 0.380 Angle : 0.754 7.622 8541 Z= 0.560 Chirality : 0.069 0.562 962 Planarity : 0.003 0.031 754 Dihedral : 23.267 173.189 2614 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % 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: 3.04 (0.39), residues: 460 helix: 2.38 (0.29), residues: 308 sheet: None (None), residues: 0 loop : 1.43 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 286 TYR 0.006 0.001 TYR B 273 PHE 0.007 0.001 PHE A 269 TRP 0.009 0.001 TRP B 67 HIS 0.006 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.38 ( 6015) covalent geometry : angle 0.75449 / 0.56 ( 8541) hydrogen bonds : bond 0.11386 / 6.72 ( 319) hydrogen bonds : angle 4.42217 / 3.36 ( 861) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 118 ASN cc_start: 0.8318 (m-40) cc_final: 0.7940 (m-40) REVERT: B 126 ARG cc_start: 0.8263 (ptp90) cc_final: 0.8004 (mtm-85) REVERT: B 212 ASN cc_start: 0.8303 (t0) cc_final: 0.7856 (t0) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0847 time to fit residues: 8.3985 Evaluate side-chains 72 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.191166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.155007 restraints weight = 7690.284| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.72 r_work: 0.3722 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6015 Z= 0.170 Angle : 0.632 6.255 8541 Z= 0.374 Chirality : 0.046 0.272 962 Planarity : 0.004 0.033 754 Dihedral : 25.870 177.599 1678 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.56 % Allowed : 8.95 % Favored : 88.49 % 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: 3.25 (0.39), residues: 460 helix: 2.56 (0.28), residues: 308 sheet: None (None), residues: 0 loop : 1.48 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 278 TYR 0.018 0.001 TYR A 175 PHE 0.012 0.001 PHE A 269 TRP 0.015 0.001 TRP B 67 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 ( 6015) covalent geometry : angle 0.63162 / 0.37 ( 8541) hydrogen bonds : bond 0.04797 / 3.19 ( 319) hydrogen bonds : angle 3.47053 / 2.54 ( 861) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8455 (tt) cc_final: 0.8251 (tp) REVERT: A 144 MET cc_start: 0.7476 (mmm) cc_final: 0.7149 (mmm) REVERT: B 118 ASN cc_start: 0.8433 (m-40) cc_final: 0.8011 (m-40) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.0746 time to fit residues: 8.0586 Evaluate side-chains 72 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 67 TRP Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 235 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 chunk 18 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 89 ASN B 141 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.192130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.156198 restraints weight = 7670.029| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.71 r_work: 0.3725 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6015 Z= 0.141 Angle : 0.591 6.755 8541 Z= 0.351 Chirality : 0.044 0.284 962 Planarity : 0.004 0.027 754 Dihedral : 25.759 177.509 1678 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.07 % Allowed : 9.46 % Favored : 87.47 % 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: 3.34 (0.38), residues: 460 helix: 2.65 (0.28), residues: 309 sheet: None (None), residues: 0 loop : 1.45 (0.52), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 278 TYR 0.017 0.001 TYR A 175 PHE 0.012 0.001 PHE A 269 TRP 0.014 0.001 TRP A 309 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 ( 6015) covalent geometry : angle 0.59055 / 0.35 ( 8541) hydrogen bonds : bond 0.04339 / 2.88 ( 319) hydrogen bonds : angle 3.28038 / 2.41 ( 861) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.153 Fit side-chains REVERT: A 112 ASP cc_start: 0.8057 (m-30) cc_final: 0.7826 (m-30) REVERT: A 144 MET cc_start: 0.7378 (mmm) cc_final: 0.7096 (mmm) REVERT: B 118 ASN cc_start: 0.8491 (m-40) cc_final: 0.8040 (m-40) outliers start: 12 outliers final: 11 residues processed: 84 average time/residue: 0.0776 time to fit residues: 8.5812 Evaluate side-chains 78 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain B residue 67 TRP Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 249 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.191346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.154809 restraints weight = 7718.240| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.71 r_work: 0.3707 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6015 Z= 0.146 Angle : 0.590 6.538 8541 Z= 0.349 Chirality : 0.044 0.279 962 Planarity : 0.004 0.027 754 Dihedral : 25.701 177.355 1678 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.81 % Allowed : 9.72 % Favored : 87.47 % 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 (0.38), residues: 460 helix: 2.57 (0.28), residues: 315 sheet: None (None), residues: 0 loop : 1.49 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.016 0.001 TYR A 175 PHE 0.014 0.002 PHE B 269 TRP 0.012 0.001 TRP B 67 HIS 0.002 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 ( 6015) covalent geometry : angle 0.59046 / 0.35 ( 8541) hydrogen bonds : bond 0.04237 / 2.87 ( 319) hydrogen bonds : angle 3.22025 / 2.37 ( 861) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.199 Fit side-chains REVERT: A 112 ASP cc_start: 0.8072 (m-30) cc_final: 0.7815 (m-30) REVERT: A 144 MET cc_start: 0.7381 (mmm) cc_final: 0.7153 (mmm) REVERT: B 118 ASN cc_start: 0.8538 (m-40) cc_final: 0.8070 (m-40) outliers start: 11 outliers final: 10 residues processed: 78 average time/residue: 0.0783 time to fit residues: 8.0084 Evaluate side-chains 78 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain B residue 67 TRP Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 249 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.186573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.148597 restraints weight = 7832.015| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.83 r_work: 0.3639 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 : 0.005 0.063 6015 Z= 0.217 Angle : 0.641 5.918 8541 Z= 0.372 Chirality : 0.047 0.277 962 Planarity : 0.004 0.031 754 Dihedral : 25.691 175.655 1678 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.81 % Allowed : 13.04 % Favored : 84.14 % 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: 2.92 (0.38), residues: 460 helix: 2.28 (0.28), residues: 315 sheet: None (None), residues: 0 loop : 1.35 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 218 TYR 0.019 0.002 TYR A 175 PHE 0.011 0.002 PHE A 109 TRP 0.011 0.001 TRP B 67 HIS 0.005 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.22 ( 6015) covalent geometry : angle 0.64149 / 0.37 ( 8541) hydrogen bonds : bond 0.04886 / 3.35 ( 319) hydrogen bonds : angle 3.37458 / 2.49 ( 861) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.113 Fit side-chains REVERT: A 112 ASP cc_start: 0.8090 (m-30) cc_final: 0.7862 (m-30) REVERT: A 139 LEU cc_start: 0.8523 (tt) cc_final: 0.8312 (tp) REVERT: A 184 ASP cc_start: 0.8228 (t70) cc_final: 0.7957 (t0) REVERT: B 118 ASN cc_start: 0.8552 (m-40) cc_final: 0.8084 (m-40) outliers start: 11 outliers final: 9 residues processed: 74 average time/residue: 0.0802 time to fit residues: 7.7367 Evaluate side-chains 72 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 67 TRP Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 235 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.188542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.151080 restraints weight = 7756.399| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.73 r_work: 0.3663 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6015 Z= 0.160 Angle : 0.595 6.040 8541 Z= 0.350 Chirality : 0.044 0.274 962 Planarity : 0.004 0.029 754 Dihedral : 25.685 176.171 1678 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.56 % Allowed : 13.30 % Favored : 84.14 % 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: 3.07 (0.39), residues: 460 helix: 2.40 (0.29), residues: 315 sheet: None (None), residues: 0 loop : 1.39 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.013 0.001 TYR A 175 PHE 0.012 0.002 PHE B 269 TRP 0.010 0.001 TRP B 67 HIS 0.004 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 ( 6015) covalent geometry : angle 0.59500 / 0.35 ( 8541) hydrogen bonds : bond 0.04312 / 2.97 ( 319) hydrogen bonds : angle 3.26166 / 2.40 ( 861) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.176 Fit side-chains REVERT: A 112 ASP cc_start: 0.8084 (m-30) cc_final: 0.7855 (m-30) REVERT: B 118 ASN cc_start: 0.8539 (m-40) cc_final: 0.8045 (m-40) outliers start: 10 outliers final: 8 residues processed: 73 average time/residue: 0.0817 time to fit residues: 7.7804 Evaluate side-chains 70 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 235 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 GLN B 256 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.188383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.150817 restraints weight = 7828.653| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.75 r_work: 0.3655 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6015 Z= 0.169 Angle : 0.611 7.099 8541 Z= 0.355 Chirality : 0.045 0.269 962 Planarity : 0.004 0.029 754 Dihedral : 25.680 176.243 1678 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.07 % Allowed : 14.07 % Favored : 82.86 % 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 (0.39), residues: 460 helix: 2.40 (0.28), residues: 315 sheet: None (None), residues: 0 loop : 1.42 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.013 0.001 TYR B 95 PHE 0.015 0.002 PHE B 269 TRP 0.007 0.001 TRP B 249 HIS 0.003 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 ( 6015) covalent geometry : angle 0.61062 / 0.35 ( 8541) hydrogen bonds : bond 0.04360 / 3.01 ( 319) hydrogen bonds : angle 3.27988 / 2.40 ( 861) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.161 Fit side-chains REVERT: A 112 ASP cc_start: 0.8112 (m-30) cc_final: 0.7887 (m-30) REVERT: B 118 ASN cc_start: 0.8544 (m-40) cc_final: 0.8038 (m-40) outliers start: 12 outliers final: 7 residues processed: 76 average time/residue: 0.0746 time to fit residues: 7.4762 Evaluate side-chains 72 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 67 TRP Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 235 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 3 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 GLN B 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.190542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.153700 restraints weight = 7735.785| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.72 r_work: 0.3690 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6015 Z= 0.140 Angle : 0.590 7.821 8541 Z= 0.343 Chirality : 0.044 0.268 962 Planarity : 0.004 0.027 754 Dihedral : 25.675 176.680 1678 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.07 % Allowed : 13.55 % Favored : 83.38 % 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 (0.39), residues: 460 helix: 2.52 (0.29), residues: 315 sheet: None (None), residues: 0 loop : 1.56 (0.54), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.011 0.001 TYR B 95 PHE 0.017 0.002 PHE B 269 TRP 0.008 0.001 TRP B 249 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 ( 6015) covalent geometry : angle 0.59008 / 0.34 ( 8541) hydrogen bonds : bond 0.04026 / 2.78 ( 319) hydrogen bonds : angle 3.17806 / 2.34 ( 861) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.177 Fit side-chains REVERT: A 108 GLN cc_start: 0.8219 (tp40) cc_final: 0.7250 (tp40) REVERT: A 112 ASP cc_start: 0.8123 (m-30) cc_final: 0.7122 (m-30) REVERT: A 230 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8327 (m) REVERT: B 118 ASN cc_start: 0.8524 (m-40) cc_final: 0.8004 (m-40) REVERT: B 247 CYS cc_start: 0.7818 (p) cc_final: 0.7618 (p) outliers start: 12 outliers final: 9 residues processed: 80 average time/residue: 0.0835 time to fit residues: 8.9272 Evaluate side-chains 76 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain B residue 67 TRP Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 235 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.190838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.154223 restraints weight = 7738.388| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.73 r_work: 0.3701 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6015 Z= 0.140 Angle : 0.595 9.354 8541 Z= 0.345 Chirality : 0.045 0.347 962 Planarity : 0.003 0.030 754 Dihedral : 25.647 176.721 1678 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.81 % Allowed : 13.30 % Favored : 83.89 % 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: 3.32 (0.39), residues: 460 helix: 2.51 (0.29), residues: 317 sheet: None (None), residues: 0 loop : 1.68 (0.55), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.007 0.001 TYR A 175 PHE 0.014 0.002 PHE B 269 TRP 0.008 0.001 TRP B 249 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 ( 6015) covalent geometry : angle 0.59454 / 0.34 ( 8541) hydrogen bonds : bond 0.04003 / 2.75 ( 319) hydrogen bonds : angle 3.13795 / 2.32 ( 861) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.170 Fit side-chains REVERT: A 230 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8335 (m) REVERT: B 118 ASN cc_start: 0.8540 (m-40) cc_final: 0.8005 (m-40) outliers start: 11 outliers final: 10 residues processed: 75 average time/residue: 0.0774 time to fit residues: 7.7433 Evaluate side-chains 76 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain B residue 67 TRP Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 235 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 7.9990 chunk 30 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 34 optimal weight: 0.0040 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.190369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.153566 restraints weight = 7818.366| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.73 r_work: 0.3688 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6015 Z= 0.154 Angle : 0.604 9.679 8541 Z= 0.347 Chirality : 0.045 0.310 962 Planarity : 0.003 0.029 754 Dihedral : 25.643 176.393 1678 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.05 % Allowed : 14.83 % Favored : 83.12 % 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 (0.39), residues: 460 helix: 2.46 (0.29), residues: 317 sheet: None (None), residues: 0 loop : 1.67 (0.55), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 218 TYR 0.026 0.002 TYR B 175 PHE 0.013 0.002 PHE B 269 TRP 0.007 0.001 TRP B 249 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 ( 6015) covalent geometry : angle 0.60410 / 0.35 ( 8541) hydrogen bonds : bond 0.04125 / 2.84 ( 319) hydrogen bonds : angle 3.19205 / 2.35 ( 861) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.164 Fit side-chains REVERT: B 118 ASN cc_start: 0.8542 (m-40) cc_final: 0.8028 (m-40) outliers start: 8 outliers final: 8 residues processed: 72 average time/residue: 0.0807 time to fit residues: 7.7257 Evaluate side-chains 74 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 67 TRP Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 235 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.188987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.151856 restraints weight = 7627.925| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.73 r_work: 0.3674 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6015 Z= 0.171 Angle : 0.630 10.649 8541 Z= 0.357 Chirality : 0.046 0.298 962 Planarity : 0.004 0.031 754 Dihedral : 25.649 176.149 1678 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.30 % Allowed : 14.83 % Favored : 82.86 % 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: 3.18 (0.39), residues: 460 helix: 2.41 (0.29), residues: 317 sheet: None (None), residues: 0 loop : 1.61 (0.55), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 286 TYR 0.020 0.002 TYR B 175 PHE 0.011 0.002 PHE B 269 TRP 0.007 0.001 TRP B 249 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 ( 6015) covalent geometry : angle 0.62996 / 0.36 ( 8541) hydrogen bonds : bond 0.04229 / 2.92 ( 319) hydrogen bonds : angle 3.23949 / 2.39 ( 861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1399.00 seconds wall clock time: 24 minutes 45.75 seconds (1485.75 seconds total)