Starting phenix.real_space_refine on Sat Apr 4 23:12:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21kl_67763/04_2026/21kl_67763_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/21kl_67763/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/21kl_67763/04_2026/21kl_67763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21kl_67763/04_2026/21kl_67763.map" model { file = "/net/cci-nas-00/data/ceres_data/21kl_67763/04_2026/21kl_67763_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21kl_67763/04_2026/21kl_67763_neut.cif" } 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-2.1rc1-6017/lib/python3.9/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: 1.39, per 1000 atoms: 0.24 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: 0.68 Conformation dependent library (CDL) restraints added in 132.1 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: 0.52 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: 0.95 Time building geometry restraints manager: 0.80 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=" CA ASP A 184 " pdb=" CB ASP A 184 " ideal model delta sigma weight residual 1.531 1.561 -0.030 1.51e-02 4.39e+03 4.04e+00 bond pdb=" P DG D 21 " pdb=" OP2 DG D 21 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.77e+00 bond pdb=" P DT E 20 " pdb=" OP1 DT E 20 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.52e+00 bond pdb=" P DT E 20 " pdb=" OP2 DT E 20 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.41e+00 bond pdb=" P DC E 23 " pdb=" OP1 DC E 23 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.26e+00 ... (remaining 6010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 8188 1.52 - 3.05: 281 3.05 - 4.57: 48 4.57 - 6.10: 22 6.10 - 7.62: 2 Bond angle restraints: 8541 Sorted by residual: angle pdb=" CB LYS B 167 " pdb=" CG LYS B 167 " pdb=" CD LYS B 167 " ideal model delta sigma weight residual 111.30 118.92 -7.62 2.30e+00 1.89e-01 1.10e+01 angle pdb=" N ASP A 184 " pdb=" CA ASP A 184 " pdb=" CB ASP A 184 " ideal model delta sigma weight residual 111.49 106.72 4.77 1.66e+00 3.63e-01 8.25e+00 angle pdb=" C ASP A 184 " pdb=" CA ASP A 184 " pdb=" CB ASP A 184 " ideal model delta sigma weight residual 110.85 115.50 -4.65 1.64e+00 3.72e-01 8.05e+00 angle pdb=" C3' DT E 28 " pdb=" C2' DT E 28 " pdb=" C1' DT E 28 " ideal model delta sigma weight residual 101.60 105.63 -4.03 1.50e+00 4.44e-01 7.21e+00 angle pdb=" O4' C C 8 " pdb=" C1' C C 8 " pdb=" N1 C C 8 " ideal model delta sigma weight residual 108.20 112.19 -3.99 1.50e+00 4.44e-01 7.07e+00 ... (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 - 0.110: 949 0.110 - 0.221: 3 0.221 - 0.331: 0 0.331 - 0.441: 0 0.441 - 0.552: 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 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.61e+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 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.56e+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 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.89e+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: 1.510 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.800 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 : 0.004 0.043 6015 Z= 0.191 Angle : 0.694 7.622 8541 Z= 0.385 Chirality : 0.062 0.552 962 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 covalent geometry : bond 0.00409 ( 6015) covalent geometry : angle 0.69371 ( 8541) hydrogen bonds : bond 0.11386 ( 319) hydrogen bonds : angle 4.42217 ( 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 : 0.118 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: 0.0819 time to fit residues: 8.1006 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 : 0.159 ------------------------------------------------------------------------------- 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: 4.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN B 89 ASN B 256 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.188957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.152403 restraints weight = 7748.635| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.74 r_work: 0.3681 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6015 Z= 0.178 Angle : 0.616 6.111 8541 Z= 0.346 Chirality : 0.038 0.148 962 Planarity : 0.004 0.033 754 Dihedral : 25.674 177.154 1678 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.56 % Allowed : 10.49 % Favored : 86.96 % 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 (0.39), residues: 460 helix: 2.61 (0.28), residues: 309 sheet: None (None), residues: 0 loop : 1.54 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 238 TYR 0.018 0.001 TYR A 175 PHE 0.012 0.002 PHE A 269 TRP 0.010 0.001 TRP B 67 HIS 0.005 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 6015) covalent geometry : angle 0.61552 ( 8541) hydrogen bonds : bond 0.04196 ( 319) hydrogen bonds : angle 3.31793 ( 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 : 0.162 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.7449 (mmm) cc_final: 0.7011 (mmt) REVERT: A 239 ASN cc_start: 0.8284 (p0) cc_final: 0.8032 (p0) REVERT: B 118 ASN cc_start: 0.8471 (m-40) cc_final: 0.8063 (m-40) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.0726 time to fit residues: 7.9426 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 : 0.107 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 0.4980 chunk 18 optimal weight: 0.0470 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN B 89 ASN B 91 GLN B 204 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.192955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.157405 restraints weight = 7713.699| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.71 r_work: 0.3738 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1947 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= 0.139 Angle : 0.556 5.516 8541 Z= 0.315 Chirality : 0.035 0.137 962 Planarity : 0.004 0.030 754 Dihedral : 25.491 177.822 1678 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.81 % Allowed : 11.00 % 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: 3.70 (0.39), residues: 460 helix: 2.83 (0.29), residues: 312 sheet: None (None), residues: 0 loop : 1.79 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 286 TYR 0.009 0.001 TYR A 273 PHE 0.016 0.002 PHE B 269 TRP 0.006 0.001 TRP B 249 HIS 0.002 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6015) covalent geometry : angle 0.55602 ( 8541) hydrogen bonds : bond 0.03723 ( 319) hydrogen bonds : angle 3.04752 ( 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: 11 poor density : 76 time to evaluate : 0.181 Fit side-chains REVERT: A 184 ASP cc_start: 0.8106 (t70) cc_final: 0.7879 (t0) REVERT: B 118 ASN cc_start: 0.8511 (m-40) cc_final: 0.8059 (m-40) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 0.0759 time to fit residues: 8.2991 Evaluate side-chains 75 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.0770 chunk 31 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN B 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.192933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.157068 restraints weight = 7711.036| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.72 r_work: 0.3734 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6015 Z= 0.141 Angle : 0.564 6.774 8541 Z= 0.314 Chirality : 0.036 0.233 962 Planarity : 0.003 0.028 754 Dihedral : 25.506 177.200 1678 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.30 % Allowed : 13.30 % Favored : 84.40 % 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: 3.78 (0.38), residues: 460 helix: 2.84 (0.28), residues: 310 sheet: None (None), residues: 0 loop : 2.00 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 286 TYR 0.017 0.001 TYR B 175 PHE 0.014 0.002 PHE B 269 TRP 0.011 0.001 TRP A 309 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6015) covalent geometry : angle 0.56361 ( 8541) hydrogen bonds : bond 0.03671 ( 319) hydrogen bonds : angle 3.02802 ( 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 82 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 95 TYR cc_start: 0.6556 (m-80) cc_final: 0.6337 (m-80) REVERT: A 108 GLN cc_start: 0.8111 (tp40) cc_final: 0.7345 (tp40) REVERT: A 112 ASP cc_start: 0.8074 (m-30) cc_final: 0.7184 (m-30) REVERT: B 86 MET cc_start: 0.6387 (tpp) cc_final: 0.6111 (mtt) REVERT: B 118 ASN cc_start: 0.8512 (m-40) cc_final: 0.8014 (m-40) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.0791 time to fit residues: 8.1489 Evaluate side-chains 75 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 30 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN B 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.192259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155768 restraints weight = 7828.578| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.74 r_work: 0.3712 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6015 Z= 0.150 Angle : 0.568 7.734 8541 Z= 0.315 Chirality : 0.035 0.188 962 Planarity : 0.003 0.027 754 Dihedral : 25.480 177.340 1678 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.05 % Allowed : 13.81 % 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: 3.60 (0.39), residues: 460 helix: 2.68 (0.28), residues: 316 sheet: None (None), residues: 0 loop : 1.90 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 286 TYR 0.014 0.001 TYR B 175 PHE 0.011 0.002 PHE B 269 TRP 0.005 0.001 TRP B 249 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6015) covalent geometry : angle 0.56754 ( 8541) hydrogen bonds : bond 0.03724 ( 319) hydrogen bonds : angle 3.08729 ( 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 80 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8176 (tp40) cc_final: 0.7586 (tp40) REVERT: A 112 ASP cc_start: 0.8110 (m-30) cc_final: 0.7406 (m-30) REVERT: B 118 ASN cc_start: 0.8499 (m-40) cc_final: 0.7987 (m-40) outliers start: 8 outliers final: 8 residues processed: 76 average time/residue: 0.0789 time to fit residues: 7.8538 Evaluate side-chains 77 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.191445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.154633 restraints weight = 7706.193| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.73 r_work: 0.3704 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2551 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= 0.153 Angle : 0.579 10.779 8541 Z= 0.314 Chirality : 0.036 0.230 962 Planarity : 0.003 0.027 754 Dihedral : 25.502 177.135 1678 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 2.56 % Allowed : 13.55 % 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: 3.53 (0.39), residues: 460 helix: 2.63 (0.28), residues: 316 sheet: None (None), residues: 0 loop : 1.90 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 286 TYR 0.017 0.001 TYR B 175 PHE 0.011 0.002 PHE B 269 TRP 0.005 0.001 TRP B 249 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6015) covalent geometry : angle 0.57920 ( 8541) hydrogen bonds : bond 0.03728 ( 319) hydrogen bonds : angle 3.11356 ( 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 80 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8169 (tp40) cc_final: 0.7578 (tp40) REVERT: A 112 ASP cc_start: 0.8062 (m-30) cc_final: 0.7337 (m-30) REVERT: B 86 MET cc_start: 0.6312 (tpp) cc_final: 0.5984 (mtt) REVERT: B 88 MET cc_start: 0.5778 (mmp) cc_final: 0.5551 (mpp) REVERT: B 118 ASN cc_start: 0.8528 (m-40) cc_final: 0.7988 (m-40) outliers start: 10 outliers final: 9 residues processed: 76 average time/residue: 0.0801 time to fit residues: 7.9752 Evaluate side-chains 75 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 67 TRP Chi-restraints excluded: chain B residue 89 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.4980 chunk 12 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.192079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.155013 restraints weight = 7766.680| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.74 r_work: 0.3705 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2703 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= 0.145 Angle : 0.568 8.648 8541 Z= 0.310 Chirality : 0.035 0.157 962 Planarity : 0.003 0.026 754 Dihedral : 25.513 177.304 1678 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.56 % Allowed : 14.83 % Favored : 82.61 % 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: 3.54 (0.39), residues: 460 helix: 2.61 (0.28), residues: 316 sheet: None (None), residues: 0 loop : 1.96 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 286 TYR 0.011 0.001 TYR A 175 PHE 0.011 0.001 PHE A 269 TRP 0.007 0.001 TRP B 249 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6015) covalent geometry : angle 0.56838 ( 8541) hydrogen bonds : bond 0.03623 ( 319) hydrogen bonds : angle 3.08392 ( 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 79 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8183 (tp40) cc_final: 0.7617 (tp40) REVERT: A 112 ASP cc_start: 0.8107 (m-30) cc_final: 0.7430 (m-30) REVERT: B 86 MET cc_start: 0.6335 (tpp) cc_final: 0.6023 (mtt) REVERT: B 88 MET cc_start: 0.5712 (mmp) cc_final: 0.5478 (mpp) REVERT: B 118 ASN cc_start: 0.8555 (m-40) cc_final: 0.7998 (m-40) outliers start: 10 outliers final: 9 residues processed: 75 average time/residue: 0.0834 time to fit residues: 8.1857 Evaluate side-chains 74 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 67 TRP Chi-restraints excluded: chain B residue 89 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 46 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.192425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.155787 restraints weight = 7682.370| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.74 r_work: 0.3711 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2786 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= 0.143 Angle : 0.577 10.184 8541 Z= 0.312 Chirality : 0.035 0.136 962 Planarity : 0.003 0.050 754 Dihedral : 25.515 177.395 1678 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.05 % Allowed : 16.62 % Favored : 81.33 % 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: 3.59 (0.39), residues: 460 helix: 2.65 (0.28), residues: 316 sheet: None (None), residues: 0 loop : 1.99 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 286 TYR 0.023 0.001 TYR B 175 PHE 0.011 0.001 PHE A 269 TRP 0.006 0.001 TRP B 249 HIS 0.002 0.001 HIS A 258 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6015) covalent geometry : angle 0.57702 ( 8541) hydrogen bonds : bond 0.03594 ( 319) hydrogen bonds : angle 3.09399 ( 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 75 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8140 (tp40) cc_final: 0.7561 (tp40) REVERT: A 112 ASP cc_start: 0.8123 (m-30) cc_final: 0.7451 (m-30) REVERT: B 86 MET cc_start: 0.6283 (tpp) cc_final: 0.6011 (mtt) REVERT: B 118 ASN cc_start: 0.8549 (m-40) cc_final: 0.7997 (m-40) outliers start: 8 outliers final: 8 residues processed: 72 average time/residue: 0.0847 time to fit residues: 7.8442 Evaluate side-chains 71 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 0.0070 chunk 16 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.192962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.156287 restraints weight = 7666.103| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.75 r_work: 0.3729 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2904 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= 0.143 Angle : 0.584 10.563 8541 Z= 0.314 Chirality : 0.035 0.136 962 Planarity : 0.003 0.046 754 Dihedral : 25.512 177.494 1678 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.56 % Allowed : 16.62 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.65 (0.39), residues: 460 helix: 2.69 (0.28), residues: 316 sheet: None (None), residues: 0 loop : 2.00 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 286 TYR 0.009 0.001 TYR A 175 PHE 0.012 0.001 PHE A 269 TRP 0.006 0.001 TRP B 249 HIS 0.002 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6015) covalent geometry : angle 0.58417 ( 8541) hydrogen bonds : bond 0.03605 ( 319) hydrogen bonds : angle 3.10863 ( 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 74 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8096 (m-30) cc_final: 0.7891 (m-30) REVERT: B 86 MET cc_start: 0.6285 (tpp) cc_final: 0.6079 (mtt) REVERT: B 118 ASN cc_start: 0.8531 (m-40) cc_final: 0.7987 (m-40) outliers start: 10 outliers final: 9 residues processed: 70 average time/residue: 0.0804 time to fit residues: 7.3200 Evaluate side-chains 73 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 67 TRP Chi-restraints excluded: chain B residue 89 ASN 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: 5.9990 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 0.0010 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN ** B 91 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 = 0.4244 r_free = 0.4244 target = 0.190049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.152051 restraints weight = 7750.506| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.76 r_work: 0.3679 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6015 Z= 0.173 Angle : 0.608 10.920 8541 Z= 0.325 Chirality : 0.036 0.138 962 Planarity : 0.003 0.032 754 Dihedral : 25.550 177.205 1678 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.56 % Allowed : 16.37 % Favored : 81.07 % 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: 3.47 (0.39), residues: 460 helix: 2.56 (0.29), residues: 315 sheet: None (None), residues: 0 loop : 1.93 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 286 TYR 0.016 0.002 TYR B 175 PHE 0.010 0.001 PHE A 269 TRP 0.006 0.001 TRP B 67 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 6015) covalent geometry : angle 0.60767 ( 8541) hydrogen bonds : bond 0.03920 ( 319) hydrogen bonds : angle 3.24267 ( 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 75 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8193 (tp40) cc_final: 0.7640 (tp40) REVERT: A 112 ASP cc_start: 0.8111 (m-30) cc_final: 0.7459 (m-30) REVERT: A 119 LYS cc_start: 0.8464 (tttt) cc_final: 0.7887 (mttm) REVERT: B 118 ASN cc_start: 0.8546 (m-40) cc_final: 0.7992 (m-40) outliers start: 10 outliers final: 9 residues processed: 71 average time/residue: 0.0846 time to fit residues: 7.7903 Evaluate side-chains 77 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 67 TRP Chi-restraints excluded: chain B residue 89 ASN 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: 0.8980 chunk 32 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.191375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.154153 restraints weight = 7558.757| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.72 r_work: 0.3702 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6015 Z= 0.154 Angle : 0.611 11.324 8541 Z= 0.323 Chirality : 0.035 0.138 962 Planarity : 0.003 0.045 754 Dihedral : 25.552 177.449 1678 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.56 % Allowed : 16.11 % Favored : 81.33 % 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: 3.49 (0.39), residues: 460 helix: 2.56 (0.29), residues: 315 sheet: None (None), residues: 0 loop : 1.97 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 286 TYR 0.013 0.001 TYR A 175 PHE 0.011 0.002 PHE A 269 TRP 0.006 0.001 TRP B 67 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6015) covalent geometry : angle 0.61080 ( 8541) hydrogen bonds : bond 0.03734 ( 319) hydrogen bonds : angle 3.19578 ( 861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1445.45 seconds wall clock time: 25 minutes 24.30 seconds (1524.30 seconds total)