Starting phenix.real_space_refine on Thu Jul 24 06:48:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n7p_24230/07_2025/7n7p_24230_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n7p_24230/07_2025/7n7p_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_24230/07_2025/7n7p_24230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n7p_24230/07_2025/7n7p_24230.map" model { file = "/net/cci-nas-00/data/ceres_data/7n7p_24230/07_2025/7n7p_24230_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n7p_24230/07_2025/7n7p_24230_neut.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.67, per 1000 atoms: 0.86 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: 1.26 Conformation dependent library (CDL) restraints added in 683.2 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: 0.46 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: 1.59 Time building geometry restraints manager: 1.49 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: 0.03 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: 1.940 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.980 Find NCS groups from input model: 0.100 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.440 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.031 0.002 TRP A 267 HIS 0.002 0.001 HIS B 30 PHE 0.034 0.002 PHE B 23 TYR 0.040 0.002 TYR A 198 ARG 0.009 0.001 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.08540 ( 451) hydrogen bonds : angle 4.28592 ( 1353) covalent geometry : bond 0.00697 ( 5552) covalent geometry : angle 1.05620 ( 7504) *********************** 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 : 0.646 Fit side-chains REVERT: A 45 ASN cc_start: 0.8018 (m110) cc_final: 0.7441 (m110) REVERT: A 56 LYS cc_start: 0.8143 (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: 0.8143 (tppt) cc_final: 0.7801 (tppp) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.2537 time to fit residues: 27.8817 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 : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.161013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115206 restraints weight = 6123.885| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.89 r_work: 0.2995 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.0992 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= 0.130 Angle : 0.481 6.572 7504 Z= 0.244 Chirality : 0.031 0.115 790 Planarity : 0.003 0.030 914 Dihedral : 11.110 77.877 802 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.30), residues: 614 helix: 2.52 (0.19), residues: 528 sheet: None (None), residues: 0 loop : -2.39 (0.53), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 192 HIS 0.003 0.001 HIS A 283 PHE 0.028 0.001 PHE A 23 TYR 0.018 0.002 TYR B 198 ARG 0.003 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 451) hydrogen bonds : angle 3.57282 ( 1353) covalent geometry : bond 0.00285 ( 5552) covalent geometry : angle 0.48053 ( 7504) *********************** 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 88 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.646 Fit side-chains REVERT: A 45 ASN cc_start: 0.8051 (m110) cc_final: 0.7513 (m110) REVERT: B 45 ASN cc_start: 0.8056 (m110) cc_final: 0.7523 (m110) outliers start: 6 outliers final: 6 residues processed: 86 average time/residue: 0.1538 time to fit residues: 18.0500 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 : 0.624 ------------------------------------------------------------------------------- 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 19 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.157890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113347 restraints weight = 6124.234| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.79 r_work: 0.2947 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5552 Z= 0.163 Angle : 0.505 6.980 7504 Z= 0.254 Chirality : 0.032 0.116 790 Planarity : 0.003 0.027 914 Dihedral : 10.234 80.613 802 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.05 % Allowed : 11.50 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.31), residues: 614 helix: 2.75 (0.20), residues: 530 sheet: None (None), residues: 0 loop : -2.25 (0.56), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 267 HIS 0.007 0.001 HIS A 283 PHE 0.021 0.001 PHE B 23 TYR 0.014 0.002 TYR A 198 ARG 0.002 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 451) hydrogen bonds : angle 3.58837 ( 1353) covalent geometry : bond 0.00374 ( 5552) covalent geometry : angle 0.50529 ( 7504) *********************** 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 92 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.622 Fit side-chains REVERT: A 36 LYS cc_start: 0.7902 (mmtm) cc_final: 0.7678 (mmtm) REVERT: A 45 ASN cc_start: 0.8010 (m110) cc_final: 0.7492 (m110) REVERT: B 36 LYS cc_start: 0.7900 (mmtm) cc_final: 0.7677 (mmtm) REVERT: B 45 ASN cc_start: 0.8008 (m110) cc_final: 0.7494 (m110) outliers start: 6 outliers final: 6 residues processed: 90 average time/residue: 0.1822 time to fit residues: 21.3761 Evaluate side-chains 84 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 59 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.157042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114208 restraints weight = 6449.284| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.07 r_work: 0.2954 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5552 Z= 0.165 Angle : 0.497 6.547 7504 Z= 0.251 Chirality : 0.032 0.112 790 Planarity : 0.003 0.026 914 Dihedral : 9.527 72.115 802 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.39 % Allowed : 12.89 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.31), residues: 614 helix: 2.87 (0.19), residues: 530 sheet: None (None), residues: 0 loop : -2.23 (0.57), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 192 HIS 0.006 0.001 HIS B 283 PHE 0.016 0.001 PHE B 23 TYR 0.012 0.002 TYR B 133 ARG 0.004 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 451) hydrogen bonds : angle 3.57066 ( 1353) covalent geometry : bond 0.00381 ( 5552) covalent geometry : angle 0.49683 ( 7504) *********************** 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 92 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.624 Fit side-chains REVERT: A 36 LYS cc_start: 0.8011 (mmtm) cc_final: 0.7712 (mmtm) REVERT: B 36 LYS cc_start: 0.7992 (mmtm) cc_final: 0.7693 (mmtm) outliers start: 8 outliers final: 6 residues processed: 88 average time/residue: 0.1809 time to fit residues: 20.6689 Evaluate side-chains 88 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.157778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114669 restraints weight = 6358.854| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.91 r_work: 0.2967 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5552 Z= 0.141 Angle : 0.524 8.607 7504 Z= 0.255 Chirality : 0.032 0.109 790 Planarity : 0.003 0.025 914 Dihedral : 9.238 69.421 802 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.09 % Allowed : 13.41 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.31), residues: 614 helix: 3.01 (0.20), residues: 530 sheet: None (None), residues: 0 loop : -2.11 (0.59), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 192 HIS 0.005 0.001 HIS A 283 PHE 0.023 0.001 PHE A 23 TYR 0.012 0.001 TYR A 133 ARG 0.006 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 451) hydrogen bonds : angle 3.47960 ( 1353) covalent geometry : bond 0.00318 ( 5552) covalent geometry : angle 0.52391 ( 7504) *********************** 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 105 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.667 Fit side-chains REVERT: A 36 LYS cc_start: 0.7948 (mmtm) cc_final: 0.7608 (mmtm) REVERT: B 36 LYS cc_start: 0.7934 (mmtm) cc_final: 0.7594 (mmtm) outliers start: 12 outliers final: 10 residues processed: 100 average time/residue: 0.1988 time to fit residues: 25.2781 Evaluate side-chains 95 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3851 r_free = 0.3851 target = 0.158754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116012 restraints weight = 6329.201| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.85 r_work: 0.3012 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1778 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= 0.134 Angle : 0.501 8.098 7504 Z= 0.248 Chirality : 0.032 0.107 790 Planarity : 0.003 0.048 914 Dihedral : 9.113 68.691 802 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.09 % Allowed : 15.51 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.31), residues: 614 helix: 3.08 (0.20), residues: 530 sheet: None (None), residues: 0 loop : -2.05 (0.60), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 192 HIS 0.004 0.001 HIS A 283 PHE 0.025 0.001 PHE B 23 TYR 0.012 0.001 TYR A 133 ARG 0.011 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 451) hydrogen bonds : angle 3.45351 ( 1353) covalent geometry : bond 0.00299 ( 5552) covalent geometry : angle 0.50052 ( 7504) *********************** 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 100 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.577 Fit side-chains REVERT: A 36 LYS cc_start: 0.7952 (mmtm) cc_final: 0.7726 (mmtp) REVERT: A 45 ASN cc_start: 0.8008 (m110) cc_final: 0.7519 (m110) REVERT: B 36 LYS cc_start: 0.7941 (mmtm) cc_final: 0.7716 (mmtp) outliers start: 12 outliers final: 9 residues processed: 96 average time/residue: 0.2184 time to fit residues: 26.5127 Evaluate side-chains 95 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 308 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.156507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.113908 restraints weight = 6349.266| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.04 r_work: 0.2961 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5552 Z= 0.172 Angle : 0.524 8.841 7504 Z= 0.263 Chirality : 0.033 0.111 790 Planarity : 0.003 0.048 914 Dihedral : 9.287 70.048 802 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.09 % Allowed : 15.85 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.58 (0.31), residues: 614 helix: 2.96 (0.19), residues: 530 sheet: None (None), residues: 0 loop : -2.01 (0.62), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 192 HIS 0.004 0.001 HIS B 283 PHE 0.027 0.002 PHE A 23 TYR 0.012 0.002 TYR A 133 ARG 0.011 0.001 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 451) hydrogen bonds : angle 3.56069 ( 1353) covalent geometry : bond 0.00400 ( 5552) covalent geometry : angle 0.52433 ( 7504) *********************** 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 98 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.590 Fit side-chains REVERT: A 36 LYS cc_start: 0.7968 (mmtm) cc_final: 0.7704 (mmtp) REVERT: B 36 LYS cc_start: 0.7955 (mmtm) cc_final: 0.7690 (mmtp) outliers start: 12 outliers final: 11 residues processed: 94 average time/residue: 0.2127 time to fit residues: 25.0932 Evaluate side-chains 95 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 140 LEU 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 140 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 21 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.158717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115630 restraints weight = 6351.459| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.88 r_work: 0.2991 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5552 Z= 0.129 Angle : 0.532 9.911 7504 Z= 0.258 Chirality : 0.032 0.108 790 Planarity : 0.003 0.045 914 Dihedral : 9.045 68.162 802 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.09 % Allowed : 16.72 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.31), residues: 614 helix: 3.09 (0.20), residues: 530 sheet: None (None), residues: 0 loop : -1.97 (0.61), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 192 HIS 0.004 0.001 HIS B 283 PHE 0.022 0.001 PHE B 23 TYR 0.012 0.001 TYR A 133 ARG 0.012 0.001 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 451) hydrogen bonds : angle 3.43928 ( 1353) covalent geometry : bond 0.00283 ( 5552) covalent geometry : angle 0.53216 ( 7504) *********************** 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 100 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.627 Fit side-chains REVERT: A 36 LYS cc_start: 0.7913 (mmtm) cc_final: 0.7649 (mmtp) REVERT: A 45 ASN cc_start: 0.8005 (m110) cc_final: 0.7495 (m110) REVERT: B 36 LYS cc_start: 0.7898 (mmtm) cc_final: 0.7637 (mmtp) outliers start: 12 outliers final: 11 residues processed: 96 average time/residue: 0.2080 time to fit residues: 25.1043 Evaluate side-chains 95 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 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 140 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.158415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114993 restraints weight = 6206.857| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.90 r_work: 0.3019 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1891 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= 0.135 Angle : 0.506 10.149 7504 Z= 0.250 Chirality : 0.032 0.107 790 Planarity : 0.003 0.042 914 Dihedral : 8.994 67.656 802 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.26 % Allowed : 16.38 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.31), residues: 614 helix: 3.12 (0.19), residues: 530 sheet: None (None), residues: 0 loop : -1.99 (0.61), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 192 HIS 0.004 0.001 HIS B 283 PHE 0.028 0.001 PHE B 23 TYR 0.012 0.001 TYR A 133 ARG 0.010 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 451) hydrogen bonds : angle 3.42014 ( 1353) covalent geometry : bond 0.00303 ( 5552) covalent geometry : angle 0.50555 ( 7504) *********************** 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 104 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.667 Fit side-chains REVERT: A 36 LYS cc_start: 0.7922 (mmtm) cc_final: 0.7648 (mmtp) REVERT: A 56 LYS cc_start: 0.8308 (tppp) cc_final: 0.7859 (tppt) REVERT: B 36 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7635 (mmtp) REVERT: B 56 LYS cc_start: 0.8317 (tppp) cc_final: 0.7867 (tppt) outliers start: 13 outliers final: 11 residues processed: 100 average time/residue: 0.2085 time to fit residues: 26.4791 Evaluate side-chains 98 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 140 LEU 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 140 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.158422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115449 restraints weight = 6387.637| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.96 r_work: 0.2986 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5552 Z= 0.145 Angle : 0.523 10.290 7504 Z= 0.261 Chirality : 0.032 0.115 790 Planarity : 0.003 0.037 914 Dihedral : 9.033 67.992 802 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.92 % Allowed : 17.07 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.31), residues: 614 helix: 3.04 (0.19), residues: 530 sheet: None (None), residues: 0 loop : -1.97 (0.61), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 192 HIS 0.004 0.001 HIS B 283 PHE 0.028 0.001 PHE A 23 TYR 0.012 0.001 TYR A 133 ARG 0.010 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 451) hydrogen bonds : angle 3.44501 ( 1353) covalent geometry : bond 0.00329 ( 5552) covalent geometry : angle 0.52280 ( 7504) ********************** 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 99 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.635 Fit side-chains REVERT: A 36 LYS cc_start: 0.7941 (mmtm) cc_final: 0.7666 (mmtp) REVERT: B 36 LYS cc_start: 0.7919 (mmtm) cc_final: 0.7641 (mmtp) outliers start: 11 outliers final: 11 residues processed: 95 average time/residue: 0.2236 time to fit residues: 27.0840 Evaluate side-chains 99 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 140 LEU 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 140 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 40 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 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 = 0.3853 r_free = 0.3853 target = 0.159389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116032 restraints weight = 6370.151| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.91 r_work: 0.3000 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1964 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= 0.130 Angle : 0.548 10.541 7504 Z= 0.266 Chirality : 0.032 0.106 790 Planarity : 0.003 0.044 914 Dihedral : 8.867 66.454 802 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.92 % Allowed : 17.42 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.31), residues: 614 helix: 3.18 (0.19), residues: 530 sheet: None (None), residues: 0 loop : -1.98 (0.60), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 192 HIS 0.003 0.001 HIS A 283 PHE 0.026 0.001 PHE B 23 TYR 0.012 0.001 TYR A 133 ARG 0.012 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 451) hydrogen bonds : angle 3.36065 ( 1353) covalent geometry : bond 0.00289 ( 5552) covalent geometry : angle 0.54751 ( 7504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3720.10 seconds wall clock time: 64 minutes 25.97 seconds (3865.97 seconds total)