Starting phenix.real_space_refine on Sat Apr 26 15:26:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gh0_40027/04_2025/8gh0_40027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gh0_40027/04_2025/8gh0_40027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gh0_40027/04_2025/8gh0_40027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gh0_40027/04_2025/8gh0_40027.map" model { file = "/net/cci-nas-00/data/ceres_data/8gh0_40027/04_2025/8gh0_40027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gh0_40027/04_2025/8gh0_40027.cif" } resolution = 4.0 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= 0.016 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 9 5.16 5 C 1287 2.51 5 N 326 2.21 5 O 332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 1954 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1939 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 153 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.30, per 1000 atoms: 1.18 Number of scatterers: 1954 At special positions: 0 Unit cell: (55.5328, 85.0346, 65.0775, 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 9 16.00 O 332 8.00 N 326 7.00 C 1287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.04 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 267.5 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 87.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'R' and resid 37 through 61 removed outlier: 3.699A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 96 removed outlier: 4.021A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix removed outlier: 3.588A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.637A pdb=" N VAL R 114 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.728A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU R 145 " --> pdb=" O TYR R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 166 removed outlier: 3.905A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE R 154 " --> pdb=" O ALA R 150 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL R 160 " --> pdb=" O MET R 156 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 172 through 175 Processing helix chain 'R' and resid 181 through 186 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.693A pdb=" N ALA R 200 " --> pdb=" O ASN R 196 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.992A pdb=" N PHE R 217 " --> pdb=" O VAL R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 299 removed outlier: 4.225A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.515A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'R' and resid 317 through 327 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 339 161 hydrogen bonds defined for protein. 480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.41 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 596 1.34 - 1.46: 518 1.46 - 1.58: 878 1.58 - 1.71: 0 1.71 - 1.83: 12 Bond restraints: 2004 Sorted by residual: bond pdb=" CA HIS R 296 " pdb=" C HIS R 296 " ideal model delta sigma weight residual 1.524 1.486 0.038 1.27e-02 6.20e+03 9.02e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.452 -0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.443 -0.049 2.00e-02 2.50e+03 5.99e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.43e+00 bond pdb=" C HIS R 296 " pdb=" N VAL R 297 " ideal model delta sigma weight residual 1.335 1.306 0.028 1.26e-02 6.30e+03 5.07e+00 ... (remaining 1999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 2562 1.10 - 2.20: 151 2.20 - 3.30: 32 3.30 - 4.40: 6 4.40 - 5.50: 8 Bond angle restraints: 2759 Sorted by residual: angle pdb=" N THR R 189 " pdb=" CA THR R 189 " pdb=" C THR R 189 " ideal model delta sigma weight residual 111.28 113.69 -2.41 1.09e+00 8.42e-01 4.89e+00 angle pdb=" CA CYS R 191 " pdb=" CB CYS R 191 " pdb=" SG CYS R 191 " ideal model delta sigma weight residual 114.40 119.24 -4.84 2.30e+00 1.89e-01 4.43e+00 angle pdb=" N ASN R 322 " pdb=" CA ASN R 322 " pdb=" C ASN R 322 " ideal model delta sigma weight residual 112.75 115.56 -2.81 1.36e+00 5.41e-01 4.28e+00 angle pdb=" CA TRP R 109 " pdb=" CB TRP R 109 " pdb=" CG TRP R 109 " ideal model delta sigma weight residual 113.60 117.46 -3.86 1.90e+00 2.77e-01 4.12e+00 angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 120.44 117.81 2.63 1.30e+00 5.92e-01 4.10e+00 ... (remaining 2754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 1043 16.85 - 33.70: 77 33.70 - 50.54: 15 50.54 - 67.39: 2 67.39 - 84.24: 2 Dihedral angle restraints: 1139 sinusoidal: 314 harmonic: 825 Sorted by residual: dihedral pdb=" CA ALA R 59 " pdb=" C ALA R 59 " pdb=" N LYS R 60 " pdb=" CA LYS R 60 " ideal model delta harmonic sigma weight residual -180.00 -161.04 -18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA TRP R 99 " pdb=" C TRP R 99 " pdb=" N THR R 100 " pdb=" CA THR R 100 " ideal model delta harmonic sigma weight residual 180.00 161.56 18.44 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LEU R 302 " pdb=" C LEU R 302 " pdb=" N ILE R 303 " pdb=" CA ILE R 303 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 1136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 214 0.033 - 0.067: 93 0.067 - 0.100: 18 0.100 - 0.133: 9 0.133 - 0.167: 2 Chirality restraints: 336 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA HIS R 296 " pdb=" N HIS R 296 " pdb=" C HIS R 296 " pdb=" CB HIS R 296 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CB VAL R 218 " pdb=" CA VAL R 218 " pdb=" CG1 VAL R 218 " pdb=" CG2 VAL R 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.46e-01 ... (remaining 333 not shown) Planarity restraints: 346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 155 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C LEU R 155 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU R 155 " -0.010 2.00e-02 2.50e+03 pdb=" N MET R 156 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 277 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C ILE R 277 " 0.026 2.00e-02 2.50e+03 pdb=" O ILE R 277 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE R 278 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 99 " 0.008 2.00e-02 2.50e+03 7.37e-03 1.36e+00 pdb=" CG TRP R 99 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP R 99 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP R 99 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 99 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 99 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 99 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 99 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 99 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP R 99 " -0.000 2.00e-02 2.50e+03 ... (remaining 343 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 760 2.88 - 3.38: 2097 3.38 - 3.89: 3039 3.89 - 4.39: 2998 4.39 - 4.90: 5005 Nonbonded interactions: 13899 Sorted by model distance: nonbonded pdb=" OD1 ASP R 130 " pdb=" N ARG R 131 " model vdw 2.374 3.120 nonbonded pdb=" O ASN R 318 " pdb=" OD1 ASN R 318 " model vdw 2.516 3.040 nonbonded pdb=" O ILE R 58 " pdb=" NE2 GLN R 65 " model vdw 2.556 3.120 nonbonded pdb=" O HIS R 296 " pdb=" O GLN R 299 " model vdw 2.558 3.040 nonbonded pdb=" O ILE R 127 " pdb=" OD1 ASP R 130 " model vdw 2.579 3.040 ... (remaining 13894 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.580 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.510 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.004 0.055 2006 Z= 0.233 Angle : 0.655 5.502 2763 Z= 0.377 Chirality : 0.041 0.167 336 Planarity : 0.004 0.027 346 Dihedral : 13.375 84.238 595 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.89 (0.51), residues: 277 helix: 1.34 (0.38), residues: 202 sheet: None (None), residues: 0 loop : -1.47 (0.62), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP R 99 HIS 0.004 0.002 HIS R 178 PHE 0.016 0.002 PHE R 108 TYR 0.007 0.001 TYR R 132 ARG 0.008 0.001 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.17925 ( 161) hydrogen bonds : angle 5.93883 ( 480) SS BOND : bond 0.00318 ( 2) SS BOND : angle 2.06936 ( 4) covalent geometry : bond 0.00426 ( 2004) covalent geometry : angle 0.65119 ( 2759) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.225 Fit side-chains REVERT: R 190 CYS cc_start: 0.6395 (t) cc_final: 0.5772 (t) REVERT: R 215 MET cc_start: 0.7844 (mmm) cc_final: 0.7401 (mtt) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0967 time to fit residues: 4.8820 Evaluate side-chains 27 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.0870 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.0570 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.138913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.124942 restraints weight = 3987.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127521 restraints weight = 2100.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.129434 restraints weight = 1311.979| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2006 Z= 0.148 Angle : 0.567 5.281 2763 Z= 0.318 Chirality : 0.041 0.148 336 Planarity : 0.004 0.028 346 Dihedral : 5.246 18.799 307 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.32 % Allowed : 17.76 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.53), residues: 277 helix: 1.92 (0.37), residues: 212 sheet: None (None), residues: 0 loop : -0.60 (0.87), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 158 HIS 0.013 0.003 HIS R 296 PHE 0.009 0.001 PHE R 108 TYR 0.013 0.001 TYR R 141 ARG 0.004 0.001 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.05750 ( 161) hydrogen bonds : angle 4.37281 ( 480) SS BOND : bond 0.00157 ( 2) SS BOND : angle 1.47416 ( 4) covalent geometry : bond 0.00279 ( 2004) covalent geometry : angle 0.56465 ( 2759) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: R 131 ARG cc_start: 0.8623 (mmm-85) cc_final: 0.8389 (mmm-85) outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 0.1075 time to fit residues: 4.7739 Evaluate side-chains 32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.122834 restraints weight = 4204.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.125314 restraints weight = 2255.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126909 restraints weight = 1411.874| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2006 Z= 0.156 Angle : 0.567 5.343 2763 Z= 0.318 Chirality : 0.041 0.168 336 Planarity : 0.004 0.028 346 Dihedral : 5.164 18.258 307 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 3.95 % Allowed : 15.79 % Favored : 80.26 % 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: 1.92 (0.52), residues: 277 helix: 1.89 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -0.77 (0.83), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 109 HIS 0.021 0.004 HIS R 296 PHE 0.010 0.001 PHE R 282 TYR 0.010 0.001 TYR R 141 ARG 0.002 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.05838 ( 161) hydrogen bonds : angle 4.27110 ( 480) SS BOND : bond 0.00108 ( 2) SS BOND : angle 1.37972 ( 4) covalent geometry : bond 0.00323 ( 2004) covalent geometry : angle 0.56526 ( 2759) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.217 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 33 average time/residue: 0.1262 time to fit residues: 5.0401 Evaluate side-chains 33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 23 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123595 restraints weight = 4099.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126084 restraints weight = 2215.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127796 restraints weight = 1391.989| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2006 Z= 0.141 Angle : 0.542 5.344 2763 Z= 0.303 Chirality : 0.041 0.160 336 Planarity : 0.004 0.026 346 Dihedral : 5.044 17.861 307 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 5.26 % Allowed : 18.42 % Favored : 76.32 % 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: 1.95 (0.52), residues: 277 helix: 1.94 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -0.89 (0.79), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 109 HIS 0.013 0.003 HIS R 296 PHE 0.010 0.001 PHE R 282 TYR 0.007 0.001 TYR R 141 ARG 0.004 0.001 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.05527 ( 161) hydrogen bonds : angle 4.14234 ( 480) SS BOND : bond 0.00072 ( 2) SS BOND : angle 1.49745 ( 4) covalent geometry : bond 0.00283 ( 2004) covalent geometry : angle 0.53983 ( 2759) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 131 ARG cc_start: 0.8699 (mmm-85) cc_final: 0.8493 (mmm-85) REVERT: R 269 HIS cc_start: 0.7660 (OUTLIER) cc_final: 0.7164 (t70) outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 0.1589 time to fit residues: 8.2098 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 269 HIS Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.123317 restraints weight = 4239.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.125914 restraints weight = 2289.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.127660 restraints weight = 1432.558| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2006 Z= 0.143 Angle : 0.545 5.348 2763 Z= 0.304 Chirality : 0.041 0.167 336 Planarity : 0.003 0.026 346 Dihedral : 4.991 17.520 307 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 8.55 % Allowed : 19.08 % Favored : 72.37 % 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: 1.88 (0.52), residues: 277 helix: 1.92 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -1.07 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 99 HIS 0.013 0.003 HIS R 296 PHE 0.011 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.05511 ( 161) hydrogen bonds : angle 4.12769 ( 480) SS BOND : bond 0.00165 ( 2) SS BOND : angle 1.43313 ( 4) covalent geometry : bond 0.00287 ( 2004) covalent geometry : angle 0.54225 ( 2759) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: R 272 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8791 (tp) outliers start: 13 outliers final: 9 residues processed: 39 average time/residue: 0.1125 time to fit residues: 5.3613 Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 269 HIS R 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.138654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125140 restraints weight = 4063.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127779 restraints weight = 2207.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.129589 restraints weight = 1393.164| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2006 Z= 0.125 Angle : 0.512 5.297 2763 Z= 0.287 Chirality : 0.040 0.166 336 Planarity : 0.003 0.025 346 Dihedral : 4.809 16.946 307 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.61 % Allowed : 25.66 % Favored : 69.74 % 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: 1.92 (0.52), residues: 277 helix: 1.95 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.13 (0.78), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 99 HIS 0.011 0.003 HIS R 296 PHE 0.011 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.05015 ( 161) hydrogen bonds : angle 4.00876 ( 480) SS BOND : bond 0.00281 ( 2) SS BOND : angle 1.62056 ( 4) covalent geometry : bond 0.00231 ( 2004) covalent geometry : angle 0.50869 ( 2759) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: R 272 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8777 (tp) outliers start: 7 outliers final: 6 residues processed: 36 average time/residue: 0.1217 time to fit residues: 5.3333 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.122158 restraints weight = 4155.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.124700 restraints weight = 2251.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.126476 restraints weight = 1423.976| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2006 Z= 0.148 Angle : 0.532 5.367 2763 Z= 0.299 Chirality : 0.041 0.167 336 Planarity : 0.003 0.026 346 Dihedral : 4.874 17.099 307 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 6.58 % Allowed : 25.00 % Favored : 68.42 % 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: 1.90 (0.52), residues: 277 helix: 1.90 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.98 (0.80), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 109 HIS 0.008 0.002 HIS R 296 PHE 0.011 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 131 Details of bonding type rmsd hydrogen bonds : bond 0.05435 ( 161) hydrogen bonds : angle 4.07981 ( 480) SS BOND : bond 0.00089 ( 2) SS BOND : angle 0.54721 ( 4) covalent geometry : bond 0.00310 ( 2004) covalent geometry : angle 0.53225 ( 2759) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.206 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 37 average time/residue: 0.1126 time to fit residues: 5.0699 Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121835 restraints weight = 4137.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124377 restraints weight = 2270.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126095 restraints weight = 1445.187| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2006 Z= 0.144 Angle : 0.532 5.375 2763 Z= 0.299 Chirality : 0.041 0.168 336 Planarity : 0.003 0.026 346 Dihedral : 4.861 17.067 307 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.26 % Allowed : 26.97 % Favored : 67.76 % 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: 1.91 (0.52), residues: 277 helix: 1.91 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.97 (0.80), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 109 HIS 0.010 0.003 HIS R 296 PHE 0.012 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.002 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.05485 ( 161) hydrogen bonds : angle 4.09355 ( 480) SS BOND : bond 0.00057 ( 2) SS BOND : angle 0.55367 ( 4) covalent geometry : bond 0.00296 ( 2004) covalent geometry : angle 0.53230 ( 2759) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.218 Fit side-chains REVERT: R 66 THR cc_start: 0.8793 (m) cc_final: 0.8584 (m) outliers start: 8 outliers final: 8 residues processed: 37 average time/residue: 0.1183 time to fit residues: 5.3863 Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121753 restraints weight = 4226.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124246 restraints weight = 2303.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.125972 restraints weight = 1462.573| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2006 Z= 0.146 Angle : 0.558 6.927 2763 Z= 0.314 Chirality : 0.041 0.169 336 Planarity : 0.003 0.025 346 Dihedral : 4.889 18.686 307 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 5.92 % Allowed : 27.63 % Favored : 66.45 % 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: 1.90 (0.52), residues: 277 helix: 1.91 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.02 (0.77), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 109 HIS 0.010 0.003 HIS R 296 PHE 0.012 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.002 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.05474 ( 161) hydrogen bonds : angle 4.08287 ( 480) SS BOND : bond 0.00393 ( 2) SS BOND : angle 0.47965 ( 4) covalent geometry : bond 0.00299 ( 2004) covalent geometry : angle 0.55820 ( 2759) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.216 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 38 average time/residue: 0.1237 time to fit residues: 5.7382 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.137167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123790 restraints weight = 4052.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126264 restraints weight = 2244.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.128011 restraints weight = 1437.592| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2006 Z= 0.131 Angle : 0.537 6.320 2763 Z= 0.301 Chirality : 0.040 0.169 336 Planarity : 0.003 0.025 346 Dihedral : 4.771 18.681 307 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 5.26 % Allowed : 27.63 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.52), residues: 277 helix: 1.97 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.95 (0.78), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 109 HIS 0.010 0.003 HIS R 296 PHE 0.012 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.002 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.05100 ( 161) hydrogen bonds : angle 3.95149 ( 480) SS BOND : bond 0.00108 ( 2) SS BOND : angle 0.38123 ( 4) covalent geometry : bond 0.00257 ( 2004) covalent geometry : angle 0.53689 ( 2759) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.200 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 37 average time/residue: 0.1177 time to fit residues: 5.2797 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122590 restraints weight = 4042.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.125072 restraints weight = 2240.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.126848 restraints weight = 1431.628| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2006 Z= 0.136 Angle : 0.547 6.084 2763 Z= 0.307 Chirality : 0.041 0.170 336 Planarity : 0.003 0.026 346 Dihedral : 4.759 18.675 307 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 5.26 % Allowed : 28.95 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.52), residues: 277 helix: 1.97 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.90 (0.78), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 109 HIS 0.006 0.002 HIS R 296 PHE 0.012 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.002 0.000 ARG R 228 Details of bonding type rmsd hydrogen bonds : bond 0.05177 ( 161) hydrogen bonds : angle 3.96782 ( 480) SS BOND : bond 0.00226 ( 2) SS BOND : angle 0.46212 ( 4) covalent geometry : bond 0.00275 ( 2004) covalent geometry : angle 0.54741 ( 2759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1130.72 seconds wall clock time: 20 minutes 19.22 seconds (1219.22 seconds total)