Starting phenix.real_space_refine on Thu Mar 6 04:23:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eir_28162/03_2025/8eir_28162.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eir_28162/03_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_28162/03_2025/8eir_28162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eir_28162/03_2025/8eir_28162.map" model { file = "/net/cci-nas-00/data/ceres_data/8eir_28162/03_2025/8eir_28162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eir_28162/03_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-5624/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: 4.22, per 1000 atoms: 0.87 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: 1.24 Conformation dependent library (CDL) restraints added in 566.9 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: 0.56 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: 1.39 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.020 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:17.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.030 ------------------------------------------------------------------------------- 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= 0.323 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 *********************** 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 : 0.587 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: 1.7629 time to fit residues: 186.6482 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 : 0.612 ------------------------------------------------------------------------------- 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 = 0.3225 r_free = 0.3225 target = 0.090788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.070098 restraints weight = 8373.922| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.70 r_work: 0.2787 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- 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= 0.193 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 *********************** 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 : 0.590 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.8317 (m-80) cc_final: 0.7933 (m-10) REVERT: A 288 GLU cc_start: 0.8324 (tp30) cc_final: 0.8100 (tm-30) REVERT: B 288 GLU cc_start: 0.8302 (tp30) cc_final: 0.8056 (tm-30) REVERT: C 7 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7070 (mt0) outliers start: 16 outliers final: 8 residues processed: 90 average time/residue: 1.7619 time to fit residues: 163.0096 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 : 0.581 ------------------------------------------------------------------------------- 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: 0.0370 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.087215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.066983 restraints weight = 8511.807| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.64 r_work: 0.2728 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4974 Z= 0.278 Angle : 0.566 8.255 6758 Z= 0.297 Chirality : 0.042 0.128 766 Planarity : 0.005 0.062 880 Dihedral : 4.594 29.733 675 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.73 % Allowed : 19.40 % 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: -0.19 (0.32), residues: 624 helix: 1.07 (0.40), residues: 174 sheet: -0.24 (0.57), residues: 76 loop : -0.66 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 207 HIS 0.007 0.002 HIS A 41 PHE 0.015 0.001 PHE A 230 TYR 0.007 0.001 TYR B 182 ARG 0.009 0.001 ARG A 60 *********************** 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 : 0.933 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.8438 (m-80) cc_final: 0.8085 (m-80) REVERT: B 236 LYS cc_start: 0.9302 (ttpt) cc_final: 0.8945 (ttpp) REVERT: B 279 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6729 (mtp180) outliers start: 20 outliers final: 6 residues processed: 84 average time/residue: 2.3326 time to fit residues: 202.2652 Evaluate side-chains 80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 279 ARG Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 3 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3186 r_free = 0.3186 target = 0.087859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.067386 restraints weight = 8486.922| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.68 r_work: 0.2736 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.2573 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= 0.191 Angle : 0.517 7.735 6758 Z= 0.267 Chirality : 0.040 0.116 766 Planarity : 0.005 0.055 880 Dihedral : 4.310 21.717 675 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.36 % Allowed : 19.96 % 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 (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: -0.06 (0.32), residues: 624 helix: 1.26 (0.41), residues: 172 sheet: -0.02 (0.58), residues: 76 loop : -0.65 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 207 HIS 0.006 0.001 HIS A 41 PHE 0.010 0.001 PHE A 230 TYR 0.007 0.001 TYR A 182 ARG 0.009 0.001 ARG A 60 *********************** 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 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 223 PHE cc_start: 0.8473 (m-80) cc_final: 0.8078 (m-10) REVERT: B 56 ASP cc_start: 0.8610 (t0) cc_final: 0.8361 (t0) REVERT: B 236 LYS cc_start: 0.9322 (ttpt) cc_final: 0.8952 (ttpp) REVERT: B 279 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6717 (mtp180) outliers start: 18 outliers final: 4 residues processed: 81 average time/residue: 2.2565 time to fit residues: 187.8461 Evaluate side-chains 78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.087662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.067222 restraints weight = 8502.265| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.69 r_work: 0.2735 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4974 Z= 0.187 Angle : 0.505 6.996 6758 Z= 0.261 Chirality : 0.040 0.117 766 Planarity : 0.005 0.053 880 Dihedral : 4.202 18.712 675 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.36 % Allowed : 19.03 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.32), residues: 624 helix: 1.33 (0.41), residues: 172 sheet: 0.13 (0.58), residues: 76 loop : -0.68 (0.30), residues: 376 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 0.010 0.001 PHE B 230 TYR 0.007 0.001 TYR B 182 ARG 0.010 0.001 ARG A 60 *********************** 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: 18 poor density : 72 time to evaluate : 0.535 Fit side-chains REVERT: A 223 PHE cc_start: 0.8524 (m-80) cc_final: 0.8160 (m-10) REVERT: B 56 ASP cc_start: 0.8651 (t0) cc_final: 0.8428 (t0) REVERT: B 236 LYS cc_start: 0.9315 (ttpt) cc_final: 0.8950 (ttpp) REVERT: B 279 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6727 (mtp180) outliers start: 18 outliers final: 6 residues processed: 82 average time/residue: 1.7531 time to fit residues: 148.1725 Evaluate side-chains 70 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 279 ARG Chi-restraints excluded: chain B residue 301 SER 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 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.088719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.068452 restraints weight = 8422.139| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.67 r_work: 0.2751 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4974 Z= 0.155 Angle : 0.494 6.926 6758 Z= 0.251 Chirality : 0.039 0.116 766 Planarity : 0.005 0.050 880 Dihedral : 4.058 16.251 675 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: -0.01 (0.32), residues: 624 helix: 1.42 (0.42), residues: 172 sheet: 0.06 (0.56), residues: 76 loop : -0.70 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 207 HIS 0.006 0.001 HIS B 64 PHE 0.007 0.001 PHE A 230 TYR 0.006 0.001 TYR A 182 ARG 0.012 0.001 ARG A 60 *********************** 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: 16 poor density : 65 time to evaluate : 0.596 Fit side-chains REVERT: A 223 PHE cc_start: 0.8541 (m-80) cc_final: 0.8167 (m-10) REVERT: A 288 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: B 288 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: B 295 ASP cc_start: 0.8697 (m-30) cc_final: 0.8426 (m-30) outliers start: 16 outliers final: 5 residues processed: 75 average time/residue: 1.6518 time to fit residues: 127.7811 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 : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 288 GLU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 304 THR 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: 0.8980 chunk 61 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 30 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.087016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.067151 restraints weight = 8461.861| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.62 r_work: 0.2729 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.2880 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= 0.233 Angle : 0.535 7.331 6758 Z= 0.275 Chirality : 0.040 0.117 766 Planarity : 0.005 0.051 880 Dihedral : 4.193 15.321 674 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.92 % Allowed : 19.40 % 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 (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: -0.10 (0.32), residues: 624 helix: 1.36 (0.42), residues: 172 sheet: -0.01 (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 B 207 HIS 0.006 0.001 HIS B 41 PHE 0.012 0.001 PHE A 230 TYR 0.008 0.001 TYR B 182 ARG 0.013 0.001 ARG A 60 *********************** 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 84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.552 Fit side-chains REVERT: A 223 PHE cc_start: 0.8580 (m-80) cc_final: 0.8227 (m-10) REVERT: A 288 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: B 279 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6728 (mtp180) REVERT: B 288 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7958 (tm-30) outliers start: 21 outliers final: 4 residues processed: 75 average time/residue: 1.9298 time to fit residues: 149.7614 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 : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 288 GLU 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: 2.9990 chunk 60 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 46 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3189 r_free = 0.3189 target = 0.088245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.068110 restraints weight = 8590.771| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.69 r_work: 0.2751 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4974 Z= 0.156 Angle : 0.504 6.938 6758 Z= 0.256 Chirality : 0.039 0.117 766 Planarity : 0.005 0.049 880 Dihedral : 3.974 15.382 674 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.87 % Allowed : 20.71 % 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: -0.03 (0.33), residues: 624 helix: 1.48 (0.42), residues: 172 sheet: -0.01 (0.56), residues: 76 loop : -0.74 (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 0.007 0.001 PHE B 223 TYR 0.007 0.001 TYR B 182 ARG 0.015 0.001 ARG A 60 *********************** 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 78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.851 Fit side-chains REVERT: A 223 PHE cc_start: 0.8571 (m-80) cc_final: 0.8254 (m-10) REVERT: A 288 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: B 288 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: D 7 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.6809 (mt0) outliers start: 10 outliers final: 3 residues processed: 74 average time/residue: 1.6994 time to fit residues: 129.8221 Evaluate side-chains 73 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 304 THR Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain D residue 7 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 0.0020 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7792 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.087236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.067067 restraints weight = 8474.063| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.68 r_work: 0.2728 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4974 Z= 0.208 Angle : 0.529 7.134 6758 Z= 0.271 Chirality : 0.040 0.117 766 Planarity : 0.005 0.051 880 Dihedral : 4.080 16.084 674 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.31 % Allowed : 21.83 % 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: -0.06 (0.33), residues: 624 helix: 1.49 (0.42), residues: 172 sheet: -0.06 (0.56), residues: 76 loop : -0.77 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 207 HIS 0.006 0.002 HIS B 64 PHE 0.010 0.001 PHE A 230 TYR 0.008 0.001 TYR B 182 ARG 0.017 0.001 ARG A 60 *********************** 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 76 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.700 Fit side-chains REVERT: A 223 PHE cc_start: 0.8615 (m-80) cc_final: 0.8297 (m-10) REVERT: B 279 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6730 (mtp180) REVERT: B 295 ASP cc_start: 0.8678 (m-30) cc_final: 0.8410 (m-30) outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 2.6020 time to fit residues: 193.1932 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 : 0.624 ------------------------------------------------------------------------------- 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 46 optimal weight: 0.0970 chunk 61 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.0000 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 overall best weight: 0.4982 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.088604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.068876 restraints weight = 8646.875| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.64 r_work: 0.2758 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4974 Z= 0.157 Angle : 0.512 6.946 6758 Z= 0.261 Chirality : 0.039 0.117 766 Planarity : 0.005 0.050 880 Dihedral : 3.955 16.451 674 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.68 % Allowed : 21.08 % 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: 0.02 (0.33), residues: 624 helix: 1.61 (0.42), residues: 170 sheet: -0.05 (0.56), residues: 76 loop : -0.73 (0.30), residues: 378 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 A 182 ARG 0.008 0.001 ARG B 60 ********************** 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 77 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.645 Fit side-chains REVERT: A 223 PHE cc_start: 0.8627 (m-80) cc_final: 0.8395 (m-10) REVERT: B 60 ARG cc_start: 0.8970 (ttm-80) cc_final: 0.8518 (mtm-85) outliers start: 9 outliers final: 3 residues processed: 75 average time/residue: 2.1461 time to fit residues: 165.8171 Evaluate side-chains 71 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.0270 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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 = 0.3181 r_free = 0.3181 target = 0.087758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.067882 restraints weight = 8731.738| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.65 r_work: 0.2734 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.3082 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= 0.200 Angle : 0.535 7.121 6758 Z= 0.274 Chirality : 0.040 0.117 766 Planarity : 0.005 0.051 880 Dihedral : 4.051 17.164 674 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.68 % Allowed : 21.27 % 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: 0.10 (0.33), residues: 624 helix: 1.85 (0.43), residues: 160 sheet: -0.11 (0.56), residues: 76 loop : -0.68 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 218 HIS 0.007 0.002 HIS A 64 PHE 0.010 0.001 PHE A 230 TYR 0.019 0.001 TYR A 154 ARG 0.018 0.001 ARG A 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5750.07 seconds wall clock time: 103 minutes 19.33 seconds (6199.33 seconds total)