Starting phenix.real_space_refine on Tue Mar 3 13:47:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n7p_24230/03_2026/7n7p_24230_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n7p_24230/03_2026/7n7p_24230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n7p_24230/03_2026/7n7p_24230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n7p_24230/03_2026/7n7p_24230.map" model { file = "/net/cci-nas-00/data/ceres_data/7n7p_24230/03_2026/7n7p_24230_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n7p_24230/03_2026/7n7p_24230_neut.cif" } resolution = 3.24 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= 0.005 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 6 5.49 5 S 32 5.16 5 C 3542 2.51 5 N 898 2.21 5 O 922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5400 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2652 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 5, 'TRANS': 307} Chain breaks: 2 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 1.54, per 1000 atoms: 0.29 Number of scatterers: 5400 At special positions: 0 Unit cell: (91.996, 91.996, 90.308, 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 32 16.00 P 6 15.00 O 922 8.00 N 898 7.00 C 3542 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: 0.49 Conformation dependent library (CDL) restraints added in 370.8 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1192 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 89.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 8 through 69 removed outlier: 3.645A pdb=" N LYS A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 101 Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 122 through 153 Processing helix chain 'A' and resid 157 through 185 removed outlier: 3.954A pdb=" N ASP A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 209 removed outlier: 4.291A pdb=" N VAL A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 254 removed outlier: 3.578A pdb=" N PHE A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N GLN A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 297 removed outlier: 3.591A pdb=" N SER A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TRP A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 305 through 335 removed outlier: 3.614A pdb=" N PHE A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Proline residue: A 313 - end of helix Processing helix chain 'B' and resid 9 through 69 removed outlier: 3.645A pdb=" N LYS B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 101 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 122 through 153 Processing helix chain 'B' and resid 157 through 185 removed outlier: 3.954A pdb=" N ASP B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 209 removed outlier: 4.291A pdb=" N VAL B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 254 removed outlier: 3.578A pdb=" N PHE B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N GLN B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 254 " --> pdb=" O ALA B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 297 removed outlier: 3.590A pdb=" N SER B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TRP B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 305 through 335 removed outlier: 3.614A pdb=" N PHE B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Proline residue: B 313 - end of helix 451 hydrogen bonds defined for protein. 1353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.81 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 802 1.31 - 1.44: 1708 1.44 - 1.56: 2986 1.56 - 1.69: 10 1.69 - 1.82: 46 Bond restraints: 5552 Sorted by residual: bond pdb=" C9P COA B 401 " pdb=" N8P COA B 401 " ideal model delta sigma weight residual 1.340 1.450 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C9P COA A 401 " pdb=" N8P COA A 401 " ideal model delta sigma weight residual 1.340 1.450 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C6A COA A 401 " pdb=" N6A COA A 401 " ideal model delta sigma weight residual 1.343 1.452 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C6A COA B 401 " pdb=" N6A COA B 401 " ideal model delta sigma weight residual 1.343 1.452 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C5P COA B 401 " pdb=" N4P COA B 401 " ideal model delta sigma weight residual 1.348 1.450 -0.102 2.00e-02 2.50e+03 2.59e+01 ... (remaining 5547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 7410 3.87 - 7.74: 66 7.74 - 11.61: 20 11.61 - 15.48: 4 15.48 - 19.35: 4 Bond angle restraints: 7504 Sorted by residual: angle pdb=" O4A COA B 401 " pdb=" P2A COA B 401 " pdb=" O5A COA B 401 " ideal model delta sigma weight residual 120.51 101.16 19.35 3.00e+00 1.11e-01 4.16e+01 angle pdb=" O4A COA A 401 " pdb=" P2A COA A 401 " pdb=" O5A COA A 401 " ideal model delta sigma weight residual 120.51 101.16 19.35 3.00e+00 1.11e-01 4.16e+01 angle pdb=" O1A COA B 401 " pdb=" P1A COA B 401 " pdb=" O2A COA B 401 " ideal model delta sigma weight residual 120.41 101.25 19.16 3.00e+00 1.11e-01 4.08e+01 angle pdb=" O1A COA A 401 " pdb=" P1A COA A 401 " pdb=" O2A COA A 401 " ideal model delta sigma weight residual 120.41 101.25 19.16 3.00e+00 1.11e-01 4.08e+01 angle pdb=" O3B COA B 401 " pdb=" P3B COA B 401 " pdb=" O8A COA B 401 " ideal model delta sigma weight residual 102.33 114.29 -11.96 3.00e+00 1.11e-01 1.59e+01 ... (remaining 7499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 2768 17.53 - 35.05: 372 35.05 - 52.58: 100 52.58 - 70.11: 32 70.11 - 87.63: 4 Dihedral angle restraints: 3276 sinusoidal: 1434 harmonic: 1842 Sorted by residual: dihedral pdb=" CA VAL B 118 " pdb=" C VAL B 118 " pdb=" N THR B 119 " pdb=" CA THR B 119 " ideal model delta harmonic sigma weight residual -180.00 -162.81 -17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL A 118 " pdb=" C VAL A 118 " pdb=" N THR A 119 " pdb=" CA THR A 119 " ideal model delta harmonic sigma weight residual -180.00 -162.81 -17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ASN B 185 " pdb=" C ASN B 185 " pdb=" N GLY B 186 " pdb=" CA GLY B 186 " ideal model delta harmonic sigma weight residual 180.00 163.42 16.58 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 3273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 640 0.045 - 0.090: 116 0.090 - 0.135: 28 0.135 - 0.179: 4 0.179 - 0.224: 2 Chirality restraints: 790 Sorted by residual: chirality pdb=" C3B COA B 401 " pdb=" C2B COA B 401 " pdb=" C4B COA B 401 " pdb=" O3B COA B 401 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C3B COA A 401 " pdb=" C2B COA A 401 " pdb=" C4B COA A 401 " pdb=" O3B COA A 401 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL A 118 " pdb=" CA VAL A 118 " pdb=" CG1 VAL A 118 " pdb=" CG2 VAL A 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.78 0.15 2.00e-01 2.50e+01 5.90e-01 ... (remaining 787 not shown) Planarity restraints: 914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 198 " -0.015 2.00e-02 2.50e+03 1.61e-02 5.18e+00 pdb=" CG TYR A 198 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 198 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 198 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 198 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 198 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 198 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 198 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 198 " 0.015 2.00e-02 2.50e+03 1.59e-02 5.08e+00 pdb=" CG TYR B 198 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 198 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 198 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 198 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 198 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 198 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 198 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 23 " -0.016 2.00e-02 2.50e+03 1.50e-02 3.91e+00 pdb=" CG PHE B 23 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 23 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 23 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 23 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 23 " -0.000 2.00e-02 2.50e+03 ... (remaining 911 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1889 2.87 - 3.38: 5386 3.38 - 3.89: 9401 3.89 - 4.39: 9988 4.39 - 4.90: 17337 Nonbonded interactions: 44001 Sorted by model distance: nonbonded pdb=" O LEU A 120 " pdb=" NZ LYS A 126 " model vdw 2.364 3.120 nonbonded pdb=" O LEU B 120 " pdb=" NZ LYS B 126 " model vdw 2.364 3.120 nonbonded pdb=" O LEU A 279 " pdb=" ND1 HIS A 283 " model vdw 2.412 3.120 nonbonded pdb=" O LEU B 279 " pdb=" ND1 HIS B 283 " model vdw 2.412 3.120 nonbonded pdb=" NE2 GLN B 237 " pdb=" O5P COA B 401 " model vdw 2.421 3.120 ... (remaining 43996 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.570 Find NCS groups from input model: 0.030 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.007 0.110 5552 Z= 0.343 Angle : 1.056 19.352 7504 Z= 0.440 Chirality : 0.040 0.224 790 Planarity : 0.004 0.039 914 Dihedral : 17.611 87.634 2084 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.35 % Allowed : 1.05 % Favored : 98.61 % 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: 1.62 (0.29), residues: 614 helix: 1.66 (0.19), residues: 526 sheet: None (None), residues: 0 loop : -2.52 (0.51), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 57 TYR 0.040 0.002 TYR A 198 PHE 0.034 0.002 PHE B 23 TRP 0.031 0.002 TRP A 267 HIS 0.002 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00697 ( 5552) covalent geometry : angle 1.05620 ( 7504) hydrogen bonds : bond 0.08540 ( 451) hydrogen bonds : angle 4.28592 ( 1353) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.207 Fit side-chains REVERT: A 45 ASN cc_start: 0.8018 (m110) cc_final: 0.7440 (m110) REVERT: A 56 LYS cc_start: 0.8144 (tppt) cc_final: 0.7817 (tppp) REVERT: B 45 ASN cc_start: 0.8021 (m110) cc_final: 0.7445 (m110) REVERT: B 56 LYS cc_start: 0.8144 (tppt) cc_final: 0.7801 (tppp) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.1013 time to fit residues: 11.1089 Evaluate side-chains 78 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 8.9990 chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.160711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114921 restraints weight = 6151.277| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.95 r_work: 0.2981 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5552 Z= 0.132 Angle : 0.482 6.610 7504 Z= 0.245 Chirality : 0.031 0.121 790 Planarity : 0.003 0.030 914 Dihedral : 11.081 78.517 802 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.05 % Allowed : 6.79 % Favored : 92.16 % 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: 2.86 (0.30), residues: 614 helix: 2.52 (0.19), residues: 528 sheet: None (None), residues: 0 loop : -2.41 (0.52), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.019 0.002 TYR B 198 PHE 0.028 0.001 PHE A 23 TRP 0.011 0.001 TRP B 192 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 5552) covalent geometry : angle 0.48223 ( 7504) hydrogen bonds : bond 0.04204 ( 451) hydrogen bonds : angle 3.57100 ( 1353) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.196 Fit side-chains REVERT: A 45 ASN cc_start: 0.8028 (m110) cc_final: 0.7501 (m110) REVERT: B 32 LEU cc_start: 0.7807 (mp) cc_final: 0.7562 (mp) REVERT: B 36 LYS cc_start: 0.7812 (mmtm) cc_final: 0.7476 (mmtm) REVERT: B 45 ASN cc_start: 0.8016 (m110) cc_final: 0.7486 (m110) outliers start: 6 outliers final: 6 residues processed: 87 average time/residue: 0.0611 time to fit residues: 7.3298 Evaluate side-chains 78 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN B 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.160628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115314 restraints weight = 6100.205| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.90 r_work: 0.2981 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5552 Z= 0.126 Angle : 0.461 6.600 7504 Z= 0.233 Chirality : 0.031 0.112 790 Planarity : 0.003 0.027 914 Dihedral : 10.277 82.809 802 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.05 % Allowed : 11.67 % Favored : 87.28 % 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: 3.43 (0.31), residues: 614 helix: 2.91 (0.20), residues: 528 sheet: None (None), residues: 0 loop : -2.25 (0.54), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 57 TYR 0.014 0.002 TYR B 198 PHE 0.021 0.001 PHE B 23 TRP 0.013 0.001 TRP A 267 HIS 0.006 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 5552) covalent geometry : angle 0.46145 ( 7504) hydrogen bonds : bond 0.04073 ( 451) hydrogen bonds : angle 3.44964 ( 1353) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.248 Fit side-chains REVERT: A 36 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7692 (mmtm) REVERT: B 36 LYS cc_start: 0.7918 (mmtm) cc_final: 0.7680 (mmtm) REVERT: B 45 ASN cc_start: 0.8038 (m110) cc_final: 0.7523 (m110) outliers start: 6 outliers final: 6 residues processed: 92 average time/residue: 0.0740 time to fit residues: 9.0911 Evaluate side-chains 86 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.159465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104947 restraints weight = 6185.955| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.58 r_work: 0.2994 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5552 Z= 0.133 Angle : 0.474 7.266 7504 Z= 0.238 Chirality : 0.031 0.111 790 Planarity : 0.003 0.026 914 Dihedral : 9.365 71.646 802 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.74 % Allowed : 11.67 % Favored : 86.59 % 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 (0.31), residues: 614 helix: 3.01 (0.19), residues: 530 sheet: None (None), residues: 0 loop : -2.28 (0.56), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 57 TYR 0.012 0.002 TYR A 133 PHE 0.022 0.001 PHE A 23 TRP 0.010 0.001 TRP A 192 HIS 0.005 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 5552) covalent geometry : angle 0.47368 ( 7504) hydrogen bonds : bond 0.04107 ( 451) hydrogen bonds : angle 3.42169 ( 1353) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.216 Fit side-chains REVERT: A 36 LYS cc_start: 0.7887 (mmtm) cc_final: 0.7596 (mmtm) REVERT: A 45 ASN cc_start: 0.8017 (m-40) cc_final: 0.7558 (m110) REVERT: B 36 LYS cc_start: 0.7854 (mmtm) cc_final: 0.7555 (mmtm) outliers start: 10 outliers final: 8 residues processed: 102 average time/residue: 0.0742 time to fit residues: 9.9078 Evaluate side-chains 94 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 chunk 54 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN B 45 ASN B 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.160676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.105757 restraints weight = 6218.263| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.61 r_work: 0.3028 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5552 Z= 0.111 Angle : 0.451 7.912 7504 Z= 0.224 Chirality : 0.030 0.107 790 Planarity : 0.003 0.026 914 Dihedral : 8.918 66.633 802 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.74 % Allowed : 13.41 % Favored : 84.84 % 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: 3.85 (0.31), residues: 614 helix: 3.19 (0.19), residues: 528 sheet: None (None), residues: 0 loop : -2.11 (0.56), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 57 TYR 0.011 0.001 TYR A 133 PHE 0.023 0.001 PHE B 23 TRP 0.010 0.001 TRP A 192 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 5552) covalent geometry : angle 0.45137 ( 7504) hydrogen bonds : bond 0.03945 ( 451) hydrogen bonds : angle 3.29721 ( 1353) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.192 Fit side-chains REVERT: A 36 LYS cc_start: 0.7829 (mmtm) cc_final: 0.7477 (mmtm) REVERT: A 45 ASN cc_start: 0.8103 (m-40) cc_final: 0.7584 (m110) REVERT: B 36 LYS cc_start: 0.7840 (mmtm) cc_final: 0.7487 (mmtm) REVERT: B 45 ASN cc_start: 0.8045 (m-40) cc_final: 0.7594 (m110) outliers start: 10 outliers final: 8 residues processed: 99 average time/residue: 0.0806 time to fit residues: 10.1927 Evaluate side-chains 94 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN B 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.159611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.116007 restraints weight = 6278.886| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.96 r_work: 0.2973 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5552 Z= 0.123 Angle : 0.506 9.249 7504 Z= 0.245 Chirality : 0.031 0.106 790 Planarity : 0.003 0.041 914 Dihedral : 8.853 66.176 802 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.74 % Allowed : 14.11 % Favored : 84.15 % 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: 3.86 (0.31), residues: 614 helix: 3.16 (0.20), residues: 532 sheet: None (None), residues: 0 loop : -2.11 (0.59), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 57 TYR 0.015 0.001 TYR A 198 PHE 0.021 0.001 PHE A 23 TRP 0.010 0.001 TRP A 192 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 5552) covalent geometry : angle 0.50552 ( 7504) hydrogen bonds : bond 0.03960 ( 451) hydrogen bonds : angle 3.31485 ( 1353) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.200 Fit side-chains REVERT: A 36 LYS cc_start: 0.7858 (mmtm) cc_final: 0.7502 (mmtm) REVERT: A 45 ASN cc_start: 0.8121 (m-40) cc_final: 0.7590 (m110) REVERT: B 36 LYS cc_start: 0.7854 (mmtm) cc_final: 0.7485 (mmtm) REVERT: B 45 ASN cc_start: 0.8097 (m-40) cc_final: 0.7597 (m110) outliers start: 10 outliers final: 7 residues processed: 101 average time/residue: 0.0872 time to fit residues: 11.2000 Evaluate side-chains 96 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 4.9990 chunk 59 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 50 optimal weight: 0.0370 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.161373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.106632 restraints weight = 6307.581| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.63 r_work: 0.3012 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5552 Z= 0.111 Angle : 0.486 10.080 7504 Z= 0.239 Chirality : 0.030 0.106 790 Planarity : 0.003 0.055 914 Dihedral : 8.699 64.603 802 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.26 % Allowed : 14.46 % Favored : 83.28 % 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: 3.97 (0.31), residues: 614 helix: 3.26 (0.19), residues: 528 sheet: None (None), residues: 0 loop : -2.00 (0.56), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 57 TYR 0.027 0.001 TYR B 198 PHE 0.022 0.001 PHE A 23 TRP 0.011 0.001 TRP B 192 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 5552) covalent geometry : angle 0.48567 ( 7504) hydrogen bonds : bond 0.03928 ( 451) hydrogen bonds : angle 3.30650 ( 1353) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.204 Fit side-chains REVERT: A 36 LYS cc_start: 0.7810 (mmtm) cc_final: 0.7441 (mmtm) REVERT: A 45 ASN cc_start: 0.8161 (m-40) cc_final: 0.7636 (m110) REVERT: A 198 TYR cc_start: 0.9012 (m-80) cc_final: 0.8792 (m-80) REVERT: B 36 LYS cc_start: 0.7807 (mmtm) cc_final: 0.7435 (mmtm) REVERT: B 45 ASN cc_start: 0.8105 (m-40) cc_final: 0.7587 (m110) outliers start: 13 outliers final: 9 residues processed: 100 average time/residue: 0.0990 time to fit residues: 12.2267 Evaluate side-chains 97 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 308 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 0.0870 chunk 46 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.161184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117444 restraints weight = 6108.817| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.94 r_work: 0.2989 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5552 Z= 0.117 Angle : 0.484 10.099 7504 Z= 0.240 Chirality : 0.030 0.106 790 Planarity : 0.003 0.051 914 Dihedral : 8.649 64.121 802 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.92 % Allowed : 14.11 % Favored : 83.97 % 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: 3.93 (0.31), residues: 614 helix: 3.21 (0.19), residues: 534 sheet: None (None), residues: 0 loop : -2.25 (0.58), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 57 TYR 0.024 0.001 TYR B 198 PHE 0.025 0.001 PHE B 23 TRP 0.010 0.001 TRP B 192 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5552) covalent geometry : angle 0.48358 ( 7504) hydrogen bonds : bond 0.03925 ( 451) hydrogen bonds : angle 3.29041 ( 1353) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.131 Fit side-chains REVERT: A 36 LYS cc_start: 0.7881 (mmtm) cc_final: 0.7597 (mmtp) REVERT: A 45 ASN cc_start: 0.8176 (m-40) cc_final: 0.7691 (m110) REVERT: A 198 TYR cc_start: 0.9045 (m-80) cc_final: 0.8805 (m-80) REVERT: B 36 LYS cc_start: 0.7877 (mmtm) cc_final: 0.7593 (mmtp) REVERT: B 45 ASN cc_start: 0.8157 (m-40) cc_final: 0.7662 (m110) REVERT: B 56 LYS cc_start: 0.8406 (tppp) cc_final: 0.8137 (tppp) outliers start: 11 outliers final: 8 residues processed: 98 average time/residue: 0.0922 time to fit residues: 11.2912 Evaluate side-chains 97 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 308 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.161232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.118497 restraints weight = 6312.301| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.07 r_work: 0.3008 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5552 Z= 0.125 Angle : 0.494 10.056 7504 Z= 0.246 Chirality : 0.031 0.106 790 Planarity : 0.004 0.052 914 Dihedral : 8.705 64.802 802 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.57 % Allowed : 14.81 % Favored : 83.62 % 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: 3.80 (0.31), residues: 614 helix: 3.11 (0.19), residues: 532 sheet: None (None), residues: 0 loop : -2.07 (0.59), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 57 TYR 0.023 0.001 TYR B 198 PHE 0.028 0.001 PHE B 23 TRP 0.022 0.001 TRP B 267 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 5552) covalent geometry : angle 0.49415 ( 7504) hydrogen bonds : bond 0.03981 ( 451) hydrogen bonds : angle 3.33146 ( 1353) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.198 Fit side-chains REVERT: A 36 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7635 (mmtp) REVERT: A 45 ASN cc_start: 0.8164 (m-40) cc_final: 0.7656 (m110) REVERT: B 36 LYS cc_start: 0.7914 (mmtm) cc_final: 0.7624 (mmtp) REVERT: B 45 ASN cc_start: 0.8122 (m-40) cc_final: 0.7575 (m110) outliers start: 9 outliers final: 9 residues processed: 98 average time/residue: 0.0833 time to fit residues: 10.3303 Evaluate side-chains 98 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.159711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116733 restraints weight = 6339.749| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.16 r_work: 0.2970 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5552 Z= 0.136 Angle : 0.513 10.575 7504 Z= 0.257 Chirality : 0.032 0.108 790 Planarity : 0.004 0.044 914 Dihedral : 8.802 65.654 802 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.74 % Allowed : 14.46 % Favored : 83.80 % 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: 3.77 (0.31), residues: 614 helix: 3.09 (0.19), residues: 532 sheet: None (None), residues: 0 loop : -2.05 (0.59), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 57 TYR 0.022 0.002 TYR B 198 PHE 0.028 0.001 PHE B 23 TRP 0.019 0.001 TRP B 267 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 5552) covalent geometry : angle 0.51299 ( 7504) hydrogen bonds : bond 0.04013 ( 451) hydrogen bonds : angle 3.38811 ( 1353) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.214 Fit side-chains REVERT: A 36 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7646 (mmtp) REVERT: A 45 ASN cc_start: 0.8147 (m-40) cc_final: 0.7641 (m110) REVERT: B 36 LYS cc_start: 0.7934 (mmtm) cc_final: 0.7656 (mmtp) REVERT: B 45 ASN cc_start: 0.8151 (m-40) cc_final: 0.7651 (m110) REVERT: B 56 LYS cc_start: 0.8393 (tppp) cc_final: 0.8157 (tppp) outliers start: 10 outliers final: 9 residues processed: 96 average time/residue: 0.0932 time to fit residues: 11.2914 Evaluate side-chains 98 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 39 optimal weight: 0.0470 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.0000 chunk 46 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 overall best weight: 0.4282 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.163104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120354 restraints weight = 6356.635| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.05 r_work: 0.3041 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5552 Z= 0.110 Angle : 0.484 10.427 7504 Z= 0.242 Chirality : 0.031 0.105 790 Planarity : 0.003 0.044 914 Dihedral : 8.579 62.906 802 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.57 % Allowed : 14.63 % Favored : 83.80 % 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: 3.82 (0.31), residues: 614 helix: 3.16 (0.20), residues: 530 sheet: None (None), residues: 0 loop : -2.18 (0.56), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 57 TYR 0.030 0.001 TYR A 198 PHE 0.024 0.001 PHE B 23 TRP 0.018 0.001 TRP A 267 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 5552) covalent geometry : angle 0.48427 ( 7504) hydrogen bonds : bond 0.03890 ( 451) hydrogen bonds : angle 3.28716 ( 1353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1769.90 seconds wall clock time: 30 minutes 51.97 seconds (1851.97 seconds total)