Starting phenix.real_space_refine on Sat May 10 03:34:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eir_28162/05_2025/8eir_28162.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eir_28162/05_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_28162/05_2025/8eir_28162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eir_28162/05_2025/8eir_28162.map" model { file = "/net/cci-nas-00/data/ceres_data/8eir_28162/05_2025/8eir_28162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eir_28162/05_2025/8eir_28162.cif" } resolution = 2.49 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= 0.037 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 3.94, per 1000 atoms: 0.81 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: 1.19 Conformation dependent library (CDL) restraints added in 644.1 milliseconds 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: 0.68 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: 1.44 Time building geometry restraints manager: 1.43 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: 0.00 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: 1.990 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.760 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.100 ------------------------------------------------------------------------------- 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 (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: -1.27 (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 TRP 0.018 0.003 TRP A 207 HIS 0.010 0.004 HIS A 41 PHE 0.022 0.003 PHE B 230 TYR 0.025 0.003 TYR A 182 ARG 0.006 0.001 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.17920 ( 191) hydrogen bonds : angle 6.80759 ( 507) covalent geometry : bond 0.00495 ( 4974) covalent geometry : angle 0.81346 ( 6758) *********************** 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 : 0.571 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: 1.7071 time to fit residues: 180.8834 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 : 0.577 ------------------------------------------------------------------------------- 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 52 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3229 r_free = 0.3229 target = 0.091077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.070772 restraints weight = 8401.650| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.65 r_work: 0.2788 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4974 Z= 0.123 Angle : 0.566 8.701 6758 Z= 0.294 Chirality : 0.041 0.131 766 Planarity : 0.005 0.068 880 Dihedral : 4.737 33.401 677 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.32 % Allowed : 1.92 % Favored : 97.76 % Rotamer: Outliers : 2.99 % Allowed : 21.46 % Favored : 75.56 % 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: -0.20 (0.32), residues: 624 helix: 0.97 (0.40), residues: 174 sheet: -0.72 (0.51), residues: 84 loop : -0.50 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 207 HIS 0.007 0.002 HIS A 64 PHE 0.009 0.001 PHE B 230 TYR 0.006 0.001 TYR A 182 ARG 0.004 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 191) hydrogen bonds : angle 5.14501 ( 507) covalent geometry : bond 0.00293 ( 4974) covalent geometry : angle 0.56559 ( 6758) *********************** 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 : 0.602 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.8315 (m-80) cc_final: 0.7932 (m-10) REVERT: A 288 GLU cc_start: 0.8318 (tp30) cc_final: 0.8094 (tm-30) REVERT: B 288 GLU cc_start: 0.8298 (tp30) cc_final: 0.8052 (tm-30) REVERT: C 7 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7075 (mt0) outliers start: 16 outliers final: 8 residues processed: 90 average time/residue: 1.9105 time to fit residues: 176.6960 Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 7 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3142 r_free = 0.3142 target = 0.085379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.065306 restraints weight = 8583.020| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.62 r_work: 0.2689 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 4974 Z= 0.249 Angle : 0.616 8.903 6758 Z= 0.327 Chirality : 0.045 0.147 766 Planarity : 0.005 0.064 880 Dihedral : 4.909 38.237 675 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.54 % Allowed : 19.59 % 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 (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: -0.31 (0.32), residues: 624 helix: 0.95 (0.40), residues: 174 sheet: -0.22 (0.56), residues: 76 loop : -0.76 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 207 HIS 0.009 0.002 HIS B 41 PHE 0.019 0.002 PHE A 230 TYR 0.008 0.002 TYR B 182 ARG 0.007 0.001 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.05526 ( 191) hydrogen bonds : angle 5.24106 ( 507) covalent geometry : bond 0.00604 ( 4974) covalent geometry : angle 0.61558 ( 6758) *********************** 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 92 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.592 Fit side-chains REVERT: A 223 PHE cc_start: 0.8485 (m-80) cc_final: 0.8131 (m-80) REVERT: B 56 ASP cc_start: 0.8665 (t0) cc_final: 0.8404 (t0) REVERT: B 236 LYS cc_start: 0.9303 (ttpt) cc_final: 0.8960 (ttpp) REVERT: B 279 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6829 (mtp180) outliers start: 19 outliers final: 4 residues processed: 84 average time/residue: 1.6713 time to fit residues: 144.5841 Evaluate side-chains 73 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 279 ARG Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 3 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.086936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.066539 restraints weight = 8491.641| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.68 r_work: 0.2725 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4974 Z= 0.133 Angle : 0.526 7.633 6758 Z= 0.274 Chirality : 0.041 0.116 766 Planarity : 0.005 0.057 880 Dihedral : 4.453 26.654 675 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.99 % Allowed : 19.78 % Favored : 77.24 % 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: -0.16 (0.32), residues: 624 helix: 1.09 (0.41), residues: 174 sheet: 0.06 (0.59), residues: 76 loop : -0.71 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 207 HIS 0.006 0.002 HIS A 41 PHE 0.010 0.001 PHE B 230 TYR 0.007 0.001 TYR A 182 ARG 0.009 0.001 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 191) hydrogen bonds : angle 4.93288 ( 507) covalent geometry : bond 0.00318 ( 4974) covalent geometry : angle 0.52623 ( 6758) *********************** 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 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.606 Fit side-chains REVERT: A 223 PHE cc_start: 0.8491 (m-80) cc_final: 0.8107 (m-10) REVERT: B 279 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6752 (mtp180) outliers start: 16 outliers final: 5 residues processed: 72 average time/residue: 1.6584 time to fit residues: 123.1711 Evaluate side-chains 71 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU 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 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 52 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3183 r_free = 0.3183 target = 0.087760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.067373 restraints weight = 8502.928| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.70 r_work: 0.2738 rms_B_bonded: 3.01 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: 0.8939 moved from start: 0.2811 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= 0.111 Angle : 0.504 7.082 6758 Z= 0.260 Chirality : 0.040 0.117 766 Planarity : 0.005 0.053 880 Dihedral : 4.194 18.662 675 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.80 % Allowed : 19.78 % 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 (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: -0.05 (0.33), residues: 624 helix: 1.24 (0.42), residues: 174 sheet: 0.20 (0.59), residues: 76 loop : -0.71 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 207 HIS 0.006 0.001 HIS B 64 PHE 0.009 0.001 PHE B 230 TYR 0.007 0.001 TYR A 182 ARG 0.010 0.001 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 191) hydrogen bonds : angle 4.77672 ( 507) covalent geometry : bond 0.00264 ( 4974) covalent geometry : angle 0.50362 ( 6758) *********************** 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 78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.590 Fit side-chains REVERT: A 223 PHE cc_start: 0.8524 (m-80) cc_final: 0.8152 (m-10) REVERT: B 56 ASP cc_start: 0.8697 (t0) cc_final: 0.8478 (t0) outliers start: 15 outliers final: 4 residues processed: 71 average time/residue: 1.6275 time to fit residues: 119.2005 Evaluate side-chains 69 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 301 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 0.0370 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3187 r_free = 0.3187 target = 0.088075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.067957 restraints weight = 8491.819| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.67 r_work: 0.2749 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4974 Z= 0.104 Angle : 0.497 7.064 6758 Z= 0.255 Chirality : 0.039 0.117 766 Planarity : 0.005 0.051 880 Dihedral : 4.093 17.161 675 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.80 % Allowed : 19.96 % Favored : 77.24 % 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: -0.05 (0.33), residues: 624 helix: 1.39 (0.42), residues: 172 sheet: 0.11 (0.57), residues: 76 loop : -0.75 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 207 HIS 0.005 0.001 HIS A 41 PHE 0.008 0.001 PHE B 230 TYR 0.007 0.001 TYR A 182 ARG 0.012 0.001 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 191) hydrogen bonds : angle 4.68487 ( 507) covalent geometry : bond 0.00250 ( 4974) covalent geometry : angle 0.49707 ( 6758) *********************** 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 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.602 Fit side-chains REVERT: A 223 PHE cc_start: 0.8542 (m-80) cc_final: 0.8156 (m-10) REVERT: B 279 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6729 (mtp180) REVERT: B 295 ASP cc_start: 0.8701 (m-30) cc_final: 0.8370 (m-30) outliers start: 15 outliers final: 3 residues processed: 72 average time/residue: 1.6971 time to fit residues: 125.9604 Evaluate side-chains 70 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER 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 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 30 optimal weight: 0.0040 chunk 12 optimal weight: 0.0060 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.5208 ------------------------------------------------------------------------------- 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 = 0.3198 r_free = 0.3198 target = 0.088634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.068944 restraints weight = 8428.629| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.62 r_work: 0.2761 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4974 Z= 0.100 Angle : 0.497 7.068 6758 Z= 0.253 Chirality : 0.039 0.117 766 Planarity : 0.005 0.050 880 Dihedral : 3.969 16.080 674 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.80 % Allowed : 20.15 % Favored : 77.05 % 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: -0.03 (0.33), residues: 624 helix: 1.48 (0.42), residues: 172 sheet: 0.09 (0.57), residues: 76 loop : -0.76 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 207 HIS 0.006 0.001 HIS A 64 PHE 0.008 0.001 PHE B 223 TYR 0.007 0.001 TYR A 182 ARG 0.014 0.001 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 191) hydrogen bonds : angle 4.61907 ( 507) covalent geometry : bond 0.00240 ( 4974) covalent geometry : angle 0.49704 ( 6758) *********************** 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 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.574 Fit side-chains REVERT: A 223 PHE cc_start: 0.8586 (m-80) cc_final: 0.8213 (m-10) REVERT: A 288 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: A 295 ASP cc_start: 0.8607 (m-30) cc_final: 0.8380 (m-30) REVERT: B 279 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6642 (mtp180) outliers start: 15 outliers final: 5 residues processed: 75 average time/residue: 1.6145 time to fit residues: 125.0058 Evaluate side-chains 72 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 A residue 304 THR 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 27 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3187 r_free = 0.3187 target = 0.088029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.068203 restraints weight = 8600.500| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.64 r_work: 0.2745 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 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= 0.116 Angle : 0.512 7.224 6758 Z= 0.261 Chirality : 0.039 0.117 766 Planarity : 0.005 0.051 880 Dihedral : 4.030 15.099 674 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.24 % Allowed : 20.71 % Favored : 77.05 % 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: -0.04 (0.33), residues: 624 helix: 1.48 (0.42), residues: 172 sheet: 0.05 (0.57), residues: 76 loop : -0.78 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 207 HIS 0.005 0.001 HIS A 41 PHE 0.009 0.001 PHE B 230 TYR 0.008 0.001 TYR B 182 ARG 0.015 0.001 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 191) hydrogen bonds : angle 4.65845 ( 507) covalent geometry : bond 0.00279 ( 4974) covalent geometry : angle 0.51173 ( 6758) *********************** 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 76 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.596 Fit side-chains REVERT: A 223 PHE cc_start: 0.8610 (m-80) cc_final: 0.8268 (m-10) REVERT: A 288 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7904 (tm-30) REVERT: B 279 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6729 (mtp180) outliers start: 12 outliers final: 6 residues processed: 71 average time/residue: 1.6968 time to fit residues: 124.2211 Evaluate side-chains 72 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 276 MET Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 304 THR 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 57 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 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 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 = 0.3169 r_free = 0.3169 target = 0.086950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.067286 restraints weight = 8501.544| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.61 r_work: 0.2736 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4974 Z= 0.145 Angle : 0.532 7.316 6758 Z= 0.275 Chirality : 0.040 0.118 766 Planarity : 0.005 0.052 880 Dihedral : 4.133 16.058 674 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.87 % Allowed : 21.08 % Favored : 77.05 % 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: -0.08 (0.33), residues: 624 helix: 1.46 (0.42), residues: 172 sheet: -0.01 (0.57), residues: 76 loop : -0.80 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 207 HIS 0.007 0.002 HIS B 64 PHE 0.011 0.001 PHE B 230 TYR 0.009 0.001 TYR B 182 ARG 0.017 0.001 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 191) hydrogen bonds : angle 4.74486 ( 507) covalent geometry : bond 0.00351 ( 4974) covalent geometry : angle 0.53206 ( 6758) *********************** 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 74 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.589 Fit side-chains REVERT: A 223 PHE cc_start: 0.8641 (m-80) cc_final: 0.8335 (m-10) REVERT: B 279 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6770 (mtp180) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 1.8918 time to fit residues: 134.2579 Evaluate side-chains 71 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 276 MET Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 279 ARG 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 46 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 0.0020 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.3180 r_free = 0.3180 target = 0.087779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.067727 restraints weight = 8639.861| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.70 r_work: 0.2744 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.3042 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= 0.108 Angle : 0.510 7.157 6758 Z= 0.261 Chirality : 0.039 0.118 766 Planarity : 0.005 0.049 880 Dihedral : 3.972 16.181 674 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.49 % Allowed : 21.27 % Favored : 77.24 % 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: 0.01 (0.33), residues: 624 helix: 1.57 (0.42), residues: 172 sheet: 0.02 (0.57), residues: 76 loop : -0.76 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 218 HIS 0.007 0.001 HIS B 64 PHE 0.008 0.001 PHE B 223 TYR 0.007 0.001 TYR B 182 ARG 0.008 0.001 ARG B 60 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 191) hydrogen bonds : angle 4.63793 ( 507) covalent geometry : bond 0.00258 ( 4974) covalent geometry : angle 0.51006 ( 6758) ********************** 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 74 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: 0.8608 (mmt) cc_final: 0.8387 (mmt) REVERT: A 223 PHE cc_start: 0.8651 (m-80) cc_final: 0.8388 (m-10) REVERT: A 295 ASP cc_start: 0.8700 (m-30) cc_final: 0.8419 (m-30) REVERT: B 279 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6724 (mtp180) outliers start: 8 outliers final: 3 residues processed: 70 average time/residue: 1.8624 time to fit residues: 134.1557 Evaluate side-chains 70 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 304 THR Chi-restraints excluded: chain B residue 279 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.0050 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- 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 = 0.3164 r_free = 0.3164 target = 0.086667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.066463 restraints weight = 8741.141| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.71 r_work: 0.2717 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4974 Z= 0.151 Angle : 0.540 7.486 6758 Z= 0.279 Chirality : 0.041 0.118 766 Planarity : 0.005 0.052 880 Dihedral : 4.135 16.869 674 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.12 % Allowed : 21.64 % Favored : 77.24 % 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: -0.08 (0.33), residues: 624 helix: 1.49 (0.42), residues: 172 sheet: -0.06 (0.57), residues: 76 loop : -0.80 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 207 HIS 0.007 0.002 HIS A 64 PHE 0.012 0.001 PHE B 230 TYR 0.009 0.001 TYR B 182 ARG 0.017 0.001 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 191) hydrogen bonds : angle 4.75588 ( 507) covalent geometry : bond 0.00363 ( 4974) covalent geometry : angle 0.53999 ( 6758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4836.60 seconds wall clock time: 84 minutes 3.75 seconds (5043.75 seconds total)