Starting phenix.real_space_refine on Fri Aug 22 15:21:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eir_28162/08_2025/8eir_28162.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eir_28162/08_2025/8eir_28162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eir_28162/08_2025/8eir_28162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eir_28162/08_2025/8eir_28162.map" model { file = "/net/cci-nas-00/data/ceres_data/8eir_28162/08_2025/8eir_28162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eir_28162/08_2025/8eir_28162.cif" } resolution = 2.49 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= 0.037 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 3080 2.51 5 N 834 2.21 5 O 914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4870 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2366 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain: "B" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2366 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 69 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 69 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Time building chain proxies: 1.32, per 1000 atoms: 0.27 Number of scatterers: 4870 At special positions: 0 Unit cell: (88.065, 70.11, 76.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 914 8.00 N 834 7.00 C 3080 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: 0.34 Conformation dependent library (CDL) restraints added in 129.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1156 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 6 sheets defined 28.8% alpha, 24.7% 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 13 through 15 No H-bonds generated for 'chain 'A' and resid 13 through 15' Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.542A pdb=" N ARG A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.808A pdb=" N LYS A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'B' and resid 13 through 15 No H-bonds generated for 'chain 'B' and resid 13 through 15' Processing helix chain 'B' and resid 41 through 44 Processing helix chain 'B' and resid 53 through 60 removed outlier: 3.579A pdb=" N ARG B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 Processing helix chain 'B' and resid 200 through 214 Processing helix chain 'B' and resid 226 through 237 removed outlier: 3.783A pdb=" N LYS B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 292 through 302 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 75 removed outlier: 4.520A pdb=" N VAL A 68 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ASN A 28 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 removed outlier: 5.550A pdb=" N HIS A 163 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR A 175 " --> pdb=" O HIS A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 129 removed outlier: 6.823A pdb=" N ALA A 116 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 125 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 114 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLN A 127 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE A 112 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 11.351A pdb=" N THR A 111 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE A 152 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 148 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY A 149 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 75 removed outlier: 4.483A pdb=" N VAL B 68 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASN B 28 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 103 removed outlier: 6.982A pdb=" N ALA B 173 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 129 removed outlier: 6.831A pdb=" N ALA B 116 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 125 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 114 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN B 127 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE B 112 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N THR B 111 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ILE B 152 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 148 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY B 149 " --> pdb=" O CYS B 160 " (cutoff:3.500A) 191 hydrogen bonds defined for protein. 507 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: 0.43 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1570 1.34 - 1.45: 705 1.45 - 1.57: 2637 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 4974 Sorted by residual: bond pdb=" CA ASN A 277 " pdb=" CB ASN A 277 " ideal model delta sigma weight residual 1.529 1.558 -0.029 1.62e-02 3.81e+03 3.18e+00 bond pdb=" CB ASN A 277 " pdb=" CG ASN A 277 " ideal model delta sigma weight residual 1.516 1.560 -0.044 2.50e-02 1.60e+03 3.09e+00 bond pdb=" C LEU A 167 " pdb=" N PRO A 168 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.68e+00 bond pdb=" CA ASN A 277 " pdb=" C ASN A 277 " ideal model delta sigma weight residual 1.526 1.541 -0.015 1.29e-02 6.01e+03 1.38e+00 bond pdb=" C LEU B 167 " pdb=" N PRO B 168 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.27e+00 ... (remaining 4969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 6567 1.99 - 3.98: 158 3.98 - 5.98: 25 5.98 - 7.97: 4 7.97 - 9.96: 4 Bond angle restraints: 6758 Sorted by residual: angle pdb=" CA ASN A 277 " pdb=" CB ASN A 277 " pdb=" CG ASN A 277 " ideal model delta sigma weight residual 112.60 116.85 -4.25 1.00e+00 1.00e+00 1.81e+01 angle pdb=" CA MET B 49 " pdb=" CB MET B 49 " pdb=" CG MET B 49 " ideal model delta sigma weight residual 114.10 121.23 -7.13 2.00e+00 2.50e-01 1.27e+01 angle pdb=" C ASN A 277 " pdb=" CA ASN A 277 " pdb=" CB ASN A 277 " ideal model delta sigma weight residual 111.80 116.89 -5.09 1.46e+00 4.69e-01 1.21e+01 angle pdb=" CA ARG B 217 " pdb=" CB ARG B 217 " pdb=" CG ARG B 217 " ideal model delta sigma weight residual 114.10 120.82 -6.72 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CB MET A 17 " pdb=" CG MET A 17 " pdb=" SD MET A 17 " ideal model delta sigma weight residual 112.70 121.99 -9.29 3.00e+00 1.11e-01 9.60e+00 ... (remaining 6753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 2554 16.91 - 33.82: 256 33.82 - 50.73: 86 50.73 - 67.64: 29 67.64 - 84.55: 3 Dihedral angle restraints: 2928 sinusoidal: 1122 harmonic: 1806 Sorted by residual: dihedral pdb=" CA ASP A 245 " pdb=" CB ASP A 245 " pdb=" CG ASP A 245 " pdb=" OD1 ASP A 245 " ideal model delta sinusoidal sigma weight residual -30.00 -86.78 56.78 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA THR A 175 " pdb=" C THR A 175 " pdb=" N ASP A 176 " pdb=" CA ASP A 176 " ideal model delta harmonic sigma weight residual 180.00 163.89 16.11 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA PHE B 181 " pdb=" C PHE B 181 " pdb=" N TYR B 182 " pdb=" CA TYR B 182 " ideal model delta harmonic sigma weight residual 180.00 163.96 16.04 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 2925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 447 0.039 - 0.077: 226 0.077 - 0.116: 81 0.116 - 0.154: 7 0.154 - 0.192: 5 Chirality restraints: 766 Sorted by residual: chirality pdb=" CA HIS A 41 " pdb=" N HIS A 41 " pdb=" C HIS A 41 " pdb=" CB HIS A 41 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CA HIS B 41 " pdb=" N HIS B 41 " pdb=" C HIS B 41 " pdb=" CB HIS B 41 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA PRO A 168 " pdb=" N PRO A 168 " pdb=" C PRO A 168 " pdb=" CB PRO A 168 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.24e-01 ... (remaining 763 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 38 " -0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO A 39 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 231 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C ASN A 231 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN A 231 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 232 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 277 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C ASN A 277 " -0.033 2.00e-02 2.50e+03 pdb=" O ASN A 277 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 278 " 0.011 2.00e-02 2.50e+03 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 4 2.55 - 3.14: 3562 3.14 - 3.72: 7054 3.72 - 4.31: 10414 4.31 - 4.90: 17751 Nonbonded interactions: 38785 Sorted by model distance: nonbonded pdb=" O ASN A 277 " pdb=" ND2 ASN A 277 " model vdw 1.960 3.120 nonbonded pdb=" N ASP B 187 " pdb=" OD1 ASP B 187 " model vdw 2.486 3.120 nonbonded pdb=" N ASP A 187 " pdb=" OD1 ASP A 187 " model vdw 2.488 3.120 nonbonded pdb=" NE2 GLN B 69 " pdb=" OE1 GLN B 74 " model vdw 2.546 3.120 nonbonded pdb=" OE2 GLU A 166 " pdb=" N SER B 1 " model vdw 2.560 3.120 ... (remaining 38780 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' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 2.230 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.320 Find NCS groups from input model: 0.040 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:5.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4974 Z= 0.206 Angle : 0.813 9.962 6758 Z= 0.441 Chirality : 0.050 0.192 766 Planarity : 0.006 0.095 880 Dihedral : 16.398 84.551 1772 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.24 % Favored : 97.44 % Rotamer: Outliers : 2.61 % Allowed : 20.90 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.30), residues: 624 helix: -0.43 (0.36), residues: 168 sheet: -1.09 (0.55), residues: 72 loop : -0.95 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 279 TYR 0.025 0.003 TYR A 182 PHE 0.022 0.003 PHE B 230 TRP 0.018 0.003 TRP A 207 HIS 0.010 0.004 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 4974) covalent geometry : angle 0.81346 ( 6758) hydrogen bonds : bond 0.17920 ( 191) hydrogen bonds : angle 6.80759 ( 507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.6750 (mtm-85) cc_final: 0.6391 (ttp-110) outliers start: 14 outliers final: 3 residues processed: 103 average time/residue: 0.7609 time to fit residues: 80.4057 Evaluate side-chains 86 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 254 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 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 64 HIS A 277 ASN B 64 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.090152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.069455 restraints weight = 8521.764| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.73 r_work: 0.2778 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4974 Z= 0.130 Angle : 0.571 8.918 6758 Z= 0.297 Chirality : 0.041 0.133 766 Planarity : 0.005 0.068 880 Dihedral : 4.758 33.338 677 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.32 % Allowed : 1.92 % Favored : 97.76 % Rotamer: Outliers : 2.99 % Allowed : 21.27 % Favored : 75.75 % 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 aren not related in a simple way. whole: -0.22 (0.32), residues: 624 helix: 0.96 (0.40), residues: 174 sheet: -0.71 (0.52), residues: 84 loop : -0.52 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 60 TYR 0.007 0.001 TYR A 182 PHE 0.009 0.001 PHE B 230 TRP 0.012 0.002 TRP A 207 HIS 0.007 0.002 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4974) covalent geometry : angle 0.57093 ( 6758) hydrogen bonds : bond 0.04078 ( 191) hydrogen bonds : angle 5.12964 ( 507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.8363 (m-80) cc_final: 0.8011 (m-80) REVERT: A 288 GLU cc_start: 0.8351 (tp30) cc_final: 0.8147 (tm-30) REVERT: B 288 GLU cc_start: 0.8314 (tp30) cc_final: 0.8072 (tm-30) REVERT: B 290 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8879 (mt-10) outliers start: 16 outliers final: 8 residues processed: 90 average time/residue: 0.8230 time to fit residues: 75.9922 Evaluate side-chains 80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.088301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.068076 restraints weight = 8559.712| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.65 r_work: 0.2741 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4974 Z= 0.138 Angle : 0.537 8.159 6758 Z= 0.279 Chirality : 0.041 0.116 766 Planarity : 0.005 0.062 880 Dihedral : 4.399 24.487 675 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.73 % Allowed : 19.78 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.32), residues: 624 helix: 1.16 (0.40), residues: 174 sheet: -0.26 (0.57), residues: 76 loop : -0.62 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 60 TYR 0.007 0.001 TYR B 182 PHE 0.013 0.001 PHE A 230 TRP 0.011 0.001 TRP B 207 HIS 0.006 0.002 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 4974) covalent geometry : angle 0.53678 ( 6758) hydrogen bonds : bond 0.04185 ( 191) hydrogen bonds : angle 4.97164 ( 507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.8430 (m-80) cc_final: 0.7992 (m-80) REVERT: B 236 LYS cc_start: 0.9299 (ttpt) cc_final: 0.8912 (ttpp) REVERT: B 279 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6682 (mtp180) REVERT: B 288 GLU cc_start: 0.8303 (tp30) cc_final: 0.8072 (tm-30) REVERT: B 290 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8895 (mt-10) REVERT: C 7 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7179 (mt0) outliers start: 20 outliers final: 8 residues processed: 84 average time/residue: 0.7476 time to fit residues: 64.6143 Evaluate side-chains 84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 7 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.086347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.066306 restraints weight = 8536.735| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.62 r_work: 0.2709 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4974 Z= 0.182 Angle : 0.556 7.973 6758 Z= 0.291 Chirality : 0.042 0.118 766 Planarity : 0.005 0.058 880 Dihedral : 4.528 26.133 675 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.17 % Allowed : 20.15 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.32), residues: 624 helix: 1.19 (0.41), residues: 172 sheet: 0.03 (0.58), residues: 76 loop : -0.73 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 60 TYR 0.008 0.001 TYR B 182 PHE 0.015 0.001 PHE A 230 TRP 0.009 0.001 TRP B 207 HIS 0.007 0.002 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 4974) covalent geometry : angle 0.55640 ( 6758) hydrogen bonds : bond 0.04614 ( 191) hydrogen bonds : angle 4.99749 ( 507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.8507 (m-80) cc_final: 0.8126 (m-10) REVERT: B 178 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8701 (mp0) REVERT: B 236 LYS cc_start: 0.9309 (ttpt) cc_final: 0.8954 (ttpp) REVERT: B 279 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6783 (mtp180) REVERT: B 288 GLU cc_start: 0.8334 (tp30) cc_final: 0.8133 (tm-30) REVERT: B 290 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8925 (mt-10) outliers start: 17 outliers final: 4 residues processed: 80 average time/residue: 0.7327 time to fit residues: 60.2022 Evaluate side-chains 77 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.087769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.067482 restraints weight = 8674.049| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.68 r_work: 0.2739 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4974 Z= 0.114 Angle : 0.505 7.111 6758 Z= 0.260 Chirality : 0.040 0.116 766 Planarity : 0.005 0.053 880 Dihedral : 4.197 18.680 675 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.17 % Allowed : 19.40 % Favored : 77.43 % 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 aren not related in a simple way. whole: -0.07 (0.32), residues: 624 helix: 1.25 (0.41), residues: 174 sheet: 0.14 (0.58), residues: 76 loop : -0.71 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 60 TYR 0.007 0.001 TYR B 182 PHE 0.009 0.001 PHE B 230 TRP 0.007 0.001 TRP B 207 HIS 0.006 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4974) covalent geometry : angle 0.50495 ( 6758) hydrogen bonds : bond 0.03558 ( 191) hydrogen bonds : angle 4.78717 ( 507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.193 Fit side-chains REVERT: A 223 PHE cc_start: 0.8538 (m-80) cc_final: 0.8166 (m-10) REVERT: B 56 ASP cc_start: 0.8667 (t0) cc_final: 0.8452 (t0) REVERT: B 236 LYS cc_start: 0.9315 (ttpt) cc_final: 0.8949 (ttpp) REVERT: B 279 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6712 (mtp180) REVERT: B 288 GLU cc_start: 0.8289 (tp30) cc_final: 0.8072 (tm-30) REVERT: B 290 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8910 (mt-10) outliers start: 17 outliers final: 5 residues processed: 81 average time/residue: 0.7702 time to fit residues: 64.0081 Evaluate side-chains 70 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.085331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.065357 restraints weight = 8844.010| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.64 r_work: 0.2682 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 4974 Z= 0.228 Angle : 0.584 7.718 6758 Z= 0.304 Chirality : 0.043 0.125 766 Planarity : 0.005 0.055 880 Dihedral : 4.599 27.689 675 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.10 % Allowed : 19.22 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.32), residues: 624 helix: 1.16 (0.41), residues: 172 sheet: -0.06 (0.56), residues: 76 loop : -0.93 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 60 TYR 0.009 0.001 TYR A 182 PHE 0.016 0.002 PHE B 230 TRP 0.007 0.001 TRP A 207 HIS 0.008 0.002 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 4974) covalent geometry : angle 0.58368 ( 6758) hydrogen bonds : bond 0.04977 ( 191) hydrogen bonds : angle 5.04073 ( 507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.212 Fit side-chains REVERT: A 178 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8711 (mp0) REVERT: A 223 PHE cc_start: 0.8602 (m-80) cc_final: 0.8234 (m-10) REVERT: A 288 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7589 (tm-30) REVERT: B 178 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8714 (mp0) REVERT: B 279 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6901 (mtp180) outliers start: 22 outliers final: 4 residues processed: 79 average time/residue: 0.6422 time to fit residues: 52.2741 Evaluate side-chains 73 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 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 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.086538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.066803 restraints weight = 8609.281| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.62 r_work: 0.2713 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4974 Z= 0.147 Angle : 0.544 7.217 6758 Z= 0.279 Chirality : 0.041 0.118 766 Planarity : 0.005 0.053 880 Dihedral : 4.364 22.297 675 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.24 % Allowed : 20.90 % Favored : 76.87 % 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 aren not related in a simple way. whole: -0.26 (0.32), residues: 624 helix: 1.25 (0.41), residues: 172 sheet: -0.03 (0.56), residues: 76 loop : -0.90 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 60 TYR 0.008 0.001 TYR A 182 PHE 0.011 0.001 PHE A 230 TRP 0.006 0.001 TRP A 207 HIS 0.006 0.002 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4974) covalent geometry : angle 0.54395 ( 6758) hydrogen bonds : bond 0.04050 ( 191) hydrogen bonds : angle 4.88345 ( 507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.127 Fit side-chains REVERT: A 49 MET cc_start: 0.8612 (mmt) cc_final: 0.8367 (mmt) REVERT: A 223 PHE cc_start: 0.8608 (m-80) cc_final: 0.8243 (m-10) REVERT: A 288 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7996 (tm-30) REVERT: B 178 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8695 (mp0) REVERT: B 279 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6819 (mtp180) outliers start: 12 outliers final: 5 residues processed: 71 average time/residue: 0.6666 time to fit residues: 48.6998 Evaluate side-chains 71 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.086844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.066740 restraints weight = 8669.873| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.69 r_work: 0.2720 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4974 Z= 0.126 Angle : 0.530 7.133 6758 Z= 0.271 Chirality : 0.040 0.118 766 Planarity : 0.005 0.051 880 Dihedral : 4.227 19.230 675 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.87 % Allowed : 21.27 % Favored : 76.87 % 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 aren not related in a simple way. whole: -0.20 (0.32), residues: 624 helix: 1.35 (0.41), residues: 172 sheet: -0.05 (0.56), residues: 76 loop : -0.87 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 60 TYR 0.008 0.001 TYR B 182 PHE 0.009 0.001 PHE A 230 TRP 0.006 0.001 TRP A 218 HIS 0.006 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 4974) covalent geometry : angle 0.53000 ( 6758) hydrogen bonds : bond 0.03702 ( 191) hydrogen bonds : angle 4.77013 ( 507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.130 Fit side-chains REVERT: A 49 MET cc_start: 0.8582 (mmt) cc_final: 0.8366 (mmt) REVERT: A 223 PHE cc_start: 0.8632 (m-80) cc_final: 0.8251 (m-10) REVERT: B 178 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8684 (mp0) REVERT: B 279 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6772 (mtp180) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 0.7676 time to fit residues: 54.4239 Evaluate side-chains 71 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 0.0980 chunk 39 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.088939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.069352 restraints weight = 8613.150| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.62 r_work: 0.2768 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4974 Z= 0.093 Angle : 0.503 7.082 6758 Z= 0.254 Chirality : 0.039 0.117 766 Planarity : 0.005 0.049 880 Dihedral : 3.982 16.404 675 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.05 % Allowed : 21.64 % Favored : 76.31 % 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 aren not related in a simple way. whole: -0.04 (0.33), residues: 624 helix: 1.54 (0.42), residues: 172 sheet: -0.01 (0.56), residues: 76 loop : -0.79 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 60 TYR 0.006 0.001 TYR B 182 PHE 0.007 0.001 PHE B 223 TRP 0.008 0.001 TRP A 218 HIS 0.007 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 4974) covalent geometry : angle 0.50339 ( 6758) hydrogen bonds : bond 0.03023 ( 191) hydrogen bonds : angle 4.58922 ( 507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.223 Fit side-chains REVERT: A 49 MET cc_start: 0.8575 (mmt) cc_final: 0.8341 (mmt) REVERT: A 223 PHE cc_start: 0.8646 (m-80) cc_final: 0.8369 (m-10) REVERT: B 60 ARG cc_start: 0.8956 (ttm-80) cc_final: 0.8494 (mtm-85) REVERT: B 178 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8704 (mp0) REVERT: B 295 ASP cc_start: 0.8689 (m-30) cc_final: 0.8476 (m-30) outliers start: 11 outliers final: 4 residues processed: 74 average time/residue: 0.7530 time to fit residues: 57.3155 Evaluate side-chains 70 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS B 164 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.087921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.068257 restraints weight = 8727.639| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.65 r_work: 0.2752 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4974 Z= 0.117 Angle : 0.526 7.203 6758 Z= 0.268 Chirality : 0.039 0.117 766 Planarity : 0.005 0.050 880 Dihedral : 4.011 17.298 674 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.68 % Allowed : 21.83 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.33), residues: 624 helix: 1.53 (0.42), residues: 172 sheet: -0.02 (0.56), residues: 76 loop : -0.77 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 60 TYR 0.007 0.001 TYR B 182 PHE 0.011 0.001 PHE B 223 TRP 0.006 0.001 TRP A 218 HIS 0.007 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 4974) covalent geometry : angle 0.52585 ( 6758) hydrogen bonds : bond 0.03467 ( 191) hydrogen bonds : angle 4.63378 ( 507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.8654 (m-80) cc_final: 0.8398 (m-10) REVERT: B 178 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8709 (mp0) REVERT: B 295 ASP cc_start: 0.8714 (m-30) cc_final: 0.8361 (m-30) outliers start: 9 outliers final: 4 residues processed: 72 average time/residue: 0.7291 time to fit residues: 54.0201 Evaluate side-chains 68 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 28 optimal weight: 0.0370 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.087880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.068138 restraints weight = 8652.083| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.64 r_work: 0.2749 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4974 Z= 0.115 Angle : 0.527 7.189 6758 Z= 0.269 Chirality : 0.040 0.117 766 Planarity : 0.005 0.050 880 Dihedral : 4.004 16.168 674 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.87 % Allowed : 21.27 % Favored : 76.87 % 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 aren not related in a simple way. whole: -0.02 (0.33), residues: 624 helix: 1.60 (0.42), residues: 170 sheet: -0.02 (0.57), residues: 76 loop : -0.78 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 60 TYR 0.008 0.001 TYR A 182 PHE 0.009 0.001 PHE A 230 TRP 0.006 0.001 TRP A 218 HIS 0.007 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4974) covalent geometry : angle 0.52722 ( 6758) hydrogen bonds : bond 0.03443 ( 191) hydrogen bonds : angle 4.61854 ( 507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2089.13 seconds wall clock time: 36 minutes 12.94 seconds (2172.94 seconds total)