Starting phenix.real_space_refine on Wed Sep 17 03:23:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh2_44530/09_2025/9bh2_44530.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh2_44530/09_2025/9bh2_44530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bh2_44530/09_2025/9bh2_44530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh2_44530/09_2025/9bh2_44530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bh2_44530/09_2025/9bh2_44530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh2_44530/09_2025/9bh2_44530.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 17 5.16 5 C 2028 2.51 5 N 498 2.21 5 O 535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3078 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3078 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 395} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.04, per 1000 atoms: 0.34 Number of scatterers: 3078 At special positions: 0 Unit cell: (67.68, 70.218, 80.37, 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 17 16.00 O 535 8.00 N 498 7.00 C 2028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 128.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 89.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 11 through 34 Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 43 through 73 removed outlier: 3.776A pdb=" N GLY A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix Processing helix chain 'A' and resid 74 through 108 Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.563A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 150 through 170 removed outlier: 3.506A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 226 through 246 Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.591A pdb=" N HIS A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.363A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 3.748A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 Processing helix chain 'A' and resid 336 through 348 removed outlier: 4.058A pdb=" N THR A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 357 through 371 Processing helix chain 'A' and resid 376 through 388 Processing helix chain 'A' and resid 389 through 416 removed outlier: 3.637A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 792 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: 0.60 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 958 1.34 - 1.46: 640 1.46 - 1.58: 1508 1.58 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 3139 Sorted by residual: bond pdb=" N LEU A 3 " pdb=" CA LEU A 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N LEU A 372 " pdb=" CA LEU A 372 " ideal model delta sigma weight residual 1.461 1.452 0.009 1.07e-02 8.73e+03 6.86e-01 bond pdb=" CB GLU A 172 " pdb=" CG GLU A 172 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.18e-01 bond pdb=" N PRO A 128 " pdb=" CA PRO A 128 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.31e-02 5.83e+03 4.62e-01 bond pdb=" C PRO A 128 " pdb=" O PRO A 128 " ideal model delta sigma weight residual 1.246 1.240 0.005 8.50e-03 1.38e+04 4.11e-01 ... (remaining 3134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 4048 0.92 - 1.84: 173 1.84 - 2.75: 33 2.75 - 3.67: 12 3.67 - 4.59: 15 Bond angle restraints: 4281 Sorted by residual: angle pdb=" C VAL A 370 " pdb=" CA VAL A 370 " pdb=" CB VAL A 370 " ideal model delta sigma weight residual 112.14 109.38 2.76 1.35e+00 5.49e-01 4.18e+00 angle pdb=" N GLN A 220 " pdb=" CA GLN A 220 " pdb=" C GLN A 220 " ideal model delta sigma weight residual 110.80 115.14 -4.34 2.13e+00 2.20e-01 4.15e+00 angle pdb=" CA GLN A 123 " pdb=" CB GLN A 123 " pdb=" CG GLN A 123 " ideal model delta sigma weight residual 114.10 118.00 -3.90 2.00e+00 2.50e-01 3.81e+00 angle pdb=" CA GLU A 172 " pdb=" CB GLU A 172 " pdb=" CG GLU A 172 " ideal model delta sigma weight residual 114.10 117.97 -3.87 2.00e+00 2.50e-01 3.74e+00 angle pdb=" N SER A 72 " pdb=" CA SER A 72 " pdb=" C SER A 72 " ideal model delta sigma weight residual 111.36 113.36 -2.00 1.09e+00 8.42e-01 3.38e+00 ... (remaining 4276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 1638 17.76 - 35.52: 156 35.52 - 53.29: 36 53.29 - 71.05: 10 71.05 - 88.81: 5 Dihedral angle restraints: 1845 sinusoidal: 668 harmonic: 1177 Sorted by residual: dihedral pdb=" CA THR A 334 " pdb=" C THR A 334 " pdb=" N VAL A 335 " pdb=" CA VAL A 335 " ideal model delta harmonic sigma weight residual 180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLU A 219 " pdb=" C GLU A 219 " pdb=" N GLN A 220 " pdb=" CA GLN A 220 " ideal model delta harmonic sigma weight residual -180.00 -163.40 -16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU A 227 " pdb=" CG GLU A 227 " pdb=" CD GLU A 227 " pdb=" OE1 GLU A 227 " ideal model delta sinusoidal sigma weight residual 0.00 -84.35 84.35 1 3.00e+01 1.11e-03 9.62e+00 ... (remaining 1842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 315 0.026 - 0.052: 119 0.052 - 0.078: 78 0.078 - 0.105: 18 0.105 - 0.131: 7 Chirality restraints: 537 Sorted by residual: chirality pdb=" CA VAL A 138 " pdb=" N VAL A 138 " pdb=" C VAL A 138 " pdb=" CB VAL A 138 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA ILE A 256 " pdb=" N ILE A 256 " pdb=" C ILE A 256 " pdb=" CB ILE A 256 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 chirality pdb=" CA VAL A 225 " pdb=" N VAL A 225 " pdb=" C VAL A 225 " pdb=" CB VAL A 225 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.19e-01 ... (remaining 534 not shown) Planarity restraints: 526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 242 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.38e+00 pdb=" C GLN A 242 " -0.020 2.00e-02 2.50e+03 pdb=" O GLN A 242 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE A 243 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 217 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C MET A 217 " 0.020 2.00e-02 2.50e+03 pdb=" O MET A 217 " -0.007 2.00e-02 2.50e+03 pdb=" N ALA A 218 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 39 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.03e+00 pdb=" C VAL A 39 " 0.018 2.00e-02 2.50e+03 pdb=" O VAL A 39 " -0.007 2.00e-02 2.50e+03 pdb=" N HIS A 40 " -0.006 2.00e-02 2.50e+03 ... (remaining 523 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 48 2.66 - 3.22: 3291 3.22 - 3.78: 5230 3.78 - 4.34: 6712 4.34 - 4.90: 11144 Nonbonded interactions: 26425 Sorted by model distance: nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 312 " model vdw 2.104 3.040 nonbonded pdb=" N GLU A 172 " pdb=" OE1 GLU A 172 " model vdw 2.110 3.120 nonbonded pdb=" OD1 ASN A 148 " pdb=" NE2 GLN A 150 " model vdw 2.113 3.120 nonbonded pdb=" O GLU A 296 " pdb=" OG SER A 300 " model vdw 2.235 3.040 nonbonded pdb=" OE1 GLU A 296 " pdb=" OH TYR A 299 " model vdw 2.330 3.040 ... (remaining 26420 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.450 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.070 Find NCS groups from input model: 0.010 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:11.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.003 0.033 3139 Z= 0.138 Angle : 0.523 4.588 4281 Z= 0.279 Chirality : 0.038 0.131 537 Planarity : 0.002 0.020 526 Dihedral : 15.814 88.811 1099 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.62 % Allowed : 19.50 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.82 (0.41), residues: 412 helix: 2.18 (0.27), residues: 352 sheet: None (None), residues: 0 loop : 0.07 (0.84), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 52 TYR 0.010 0.001 TYR A 299 PHE 0.006 0.001 PHE A 157 HIS 0.004 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3139) covalent geometry : angle 0.52343 ( 4281) hydrogen bonds : bond 0.11483 ( 266) hydrogen bonds : angle 5.14965 ( 792) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.083 Fit side-chains REVERT: A 33 TYR cc_start: 0.8424 (m-80) cc_final: 0.8162 (m-80) REVERT: A 61 ILE cc_start: 0.8054 (tt) cc_final: 0.7778 (tt) REVERT: A 91 LEU cc_start: 0.8373 (tt) cc_final: 0.8157 (tp) REVERT: A 179 SER cc_start: 0.7689 (t) cc_final: 0.7258 (p) REVERT: A 311 MET cc_start: 0.7570 (mmp) cc_final: 0.7303 (mmt) REVERT: A 369 SER cc_start: 0.8718 (t) cc_final: 0.8414 (p) outliers start: 2 outliers final: 0 residues processed: 90 average time/residue: 0.3718 time to fit residues: 34.7116 Evaluate side-chains 76 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.0870 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 123 GLN A 203 GLN A 338 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.107226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.101097 restraints weight = 5541.276| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.53 r_work: 0.3442 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3139 Z= 0.174 Angle : 0.620 6.016 4281 Z= 0.314 Chirality : 0.045 0.317 537 Planarity : 0.004 0.033 526 Dihedral : 3.885 21.939 440 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.88 % Allowed : 18.58 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.39), residues: 412 helix: 2.00 (0.26), residues: 353 sheet: None (None), residues: 0 loop : 0.14 (0.84), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 397 TYR 0.025 0.002 TYR A 299 PHE 0.011 0.002 PHE A 323 HIS 0.003 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 3139) covalent geometry : angle 0.61953 ( 4281) hydrogen bonds : bond 0.04480 ( 266) hydrogen bonds : angle 4.58819 ( 792) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.137 Fit side-chains REVERT: A 10 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7888 (t80) REVERT: A 59 MET cc_start: 0.8247 (mmm) cc_final: 0.7988 (tpt) REVERT: A 61 ILE cc_start: 0.8431 (tt) cc_final: 0.8120 (tt) REVERT: A 179 SER cc_start: 0.8183 (t) cc_final: 0.7967 (p) REVERT: A 245 LEU cc_start: 0.7959 (mt) cc_final: 0.7692 (mt) outliers start: 19 outliers final: 3 residues processed: 94 average time/residue: 0.3441 time to fit residues: 33.6553 Evaluate side-chains 81 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 295 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.0370 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 0.0970 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.106221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.100177 restraints weight = 5468.255| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.51 r_work: 0.3427 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3139 Z= 0.184 Angle : 0.627 7.787 4281 Z= 0.312 Chirality : 0.044 0.231 537 Planarity : 0.004 0.042 526 Dihedral : 3.974 22.782 440 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.57 % Allowed : 18.27 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.39), residues: 412 helix: 1.78 (0.25), residues: 353 sheet: None (None), residues: 0 loop : 0.33 (0.85), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 397 TYR 0.023 0.002 TYR A 299 PHE 0.013 0.002 PHE A 323 HIS 0.004 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 3139) covalent geometry : angle 0.62691 ( 4281) hydrogen bonds : bond 0.04431 ( 266) hydrogen bonds : angle 4.60966 ( 792) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.116 Fit side-chains REVERT: A 10 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.7883 (t80) REVERT: A 196 LYS cc_start: 0.8132 (mmtt) cc_final: 0.6908 (pttt) REVERT: A 245 LEU cc_start: 0.8047 (mt) cc_final: 0.7828 (mp) outliers start: 18 outliers final: 8 residues processed: 94 average time/residue: 0.4002 time to fit residues: 39.0033 Evaluate side-chains 82 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 333 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 chunk 7 optimal weight: 0.0970 chunk 39 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 15 optimal weight: 0.2980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.107181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101039 restraints weight = 5300.771| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.50 r_work: 0.3437 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3139 Z= 0.155 Angle : 0.597 6.847 4281 Z= 0.299 Chirality : 0.045 0.339 537 Planarity : 0.004 0.046 526 Dihedral : 3.985 22.634 440 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.57 % Allowed : 21.67 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.38), residues: 412 helix: 1.73 (0.25), residues: 353 sheet: None (None), residues: 0 loop : 0.36 (0.86), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 287 TYR 0.023 0.002 TYR A 299 PHE 0.016 0.001 PHE A 323 HIS 0.003 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3139) covalent geometry : angle 0.59658 ( 4281) hydrogen bonds : bond 0.04197 ( 266) hydrogen bonds : angle 4.64597 ( 792) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.083 Fit side-chains REVERT: A 10 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7986 (t80) REVERT: A 33 TYR cc_start: 0.8423 (m-80) cc_final: 0.8222 (m-80) REVERT: A 61 ILE cc_start: 0.8341 (tt) cc_final: 0.8120 (tt) REVERT: A 196 LYS cc_start: 0.8146 (mmtt) cc_final: 0.6894 (pttt) REVERT: A 323 PHE cc_start: 0.8004 (t80) cc_final: 0.7796 (t80) REVERT: A 390 ASP cc_start: 0.8204 (t0) cc_final: 0.7983 (t0) outliers start: 18 outliers final: 5 residues processed: 84 average time/residue: 0.3762 time to fit residues: 32.8525 Evaluate side-chains 71 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.3980 chunk 38 optimal weight: 0.0670 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 14 optimal weight: 0.0670 chunk 5 optimal weight: 0.0980 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 0.1856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.108994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.102740 restraints weight = 5415.576| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.53 r_work: 0.3466 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3139 Z= 0.131 Angle : 0.569 6.787 4281 Z= 0.281 Chirality : 0.041 0.150 537 Planarity : 0.004 0.046 526 Dihedral : 3.896 21.372 440 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.26 % Allowed : 21.05 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.39), residues: 412 helix: 1.84 (0.25), residues: 353 sheet: None (None), residues: 0 loop : 0.38 (0.85), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 397 TYR 0.022 0.002 TYR A 299 PHE 0.014 0.001 PHE A 323 HIS 0.002 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3139) covalent geometry : angle 0.56871 ( 4281) hydrogen bonds : bond 0.03939 ( 266) hydrogen bonds : angle 4.51997 ( 792) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.118 Fit side-chains REVERT: A 10 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.8050 (t80) REVERT: A 55 LYS cc_start: 0.6122 (OUTLIER) cc_final: 0.5003 (ttpp) REVERT: A 414 LYS cc_start: 0.8015 (tppp) cc_final: 0.7747 (tttm) outliers start: 17 outliers final: 4 residues processed: 81 average time/residue: 0.3306 time to fit residues: 27.9100 Evaluate side-chains 77 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 19 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 0.0770 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.107953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.101782 restraints weight = 5379.607| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.51 r_work: 0.3449 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3139 Z= 0.166 Angle : 0.646 8.397 4281 Z= 0.310 Chirality : 0.045 0.332 537 Planarity : 0.005 0.042 526 Dihedral : 3.941 21.879 440 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 5.88 % Allowed : 20.12 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.38), residues: 412 helix: 1.79 (0.25), residues: 353 sheet: None (None), residues: 0 loop : 0.39 (0.84), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 397 TYR 0.022 0.002 TYR A 299 PHE 0.028 0.002 PHE A 323 HIS 0.003 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 3139) covalent geometry : angle 0.64591 ( 4281) hydrogen bonds : bond 0.04134 ( 266) hydrogen bonds : angle 4.62390 ( 792) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.123 Fit side-chains REVERT: A 10 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.8113 (t80) REVERT: A 33 TYR cc_start: 0.8437 (m-80) cc_final: 0.8230 (m-80) REVERT: A 55 LYS cc_start: 0.6317 (OUTLIER) cc_final: 0.5253 (ttpt) REVERT: A 244 LEU cc_start: 0.7685 (mm) cc_final: 0.7464 (mp) REVERT: A 323 PHE cc_start: 0.8047 (t80) cc_final: 0.7807 (t80) REVERT: A 414 LYS cc_start: 0.8143 (tppp) cc_final: 0.7887 (tttm) outliers start: 19 outliers final: 7 residues processed: 78 average time/residue: 0.2766 time to fit residues: 22.7350 Evaluate side-chains 76 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 361 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 5 optimal weight: 0.0870 chunk 24 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.107307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101017 restraints weight = 5468.199| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.58 r_work: 0.3435 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3139 Z= 0.177 Angle : 0.633 7.385 4281 Z= 0.307 Chirality : 0.043 0.125 537 Planarity : 0.005 0.041 526 Dihedral : 3.975 21.498 440 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 6.50 % Allowed : 20.43 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.38), residues: 412 helix: 1.77 (0.25), residues: 351 sheet: None (None), residues: 0 loop : 0.08 (0.82), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 397 TYR 0.023 0.002 TYR A 299 PHE 0.026 0.002 PHE A 323 HIS 0.004 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 3139) covalent geometry : angle 0.63265 ( 4281) hydrogen bonds : bond 0.04208 ( 266) hydrogen bonds : angle 4.66151 ( 792) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.103 Fit side-chains REVERT: A 10 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.8122 (t80) REVERT: A 49 LEU cc_start: 0.8489 (tm) cc_final: 0.8224 (tp) REVERT: A 55 LYS cc_start: 0.6322 (OUTLIER) cc_final: 0.5227 (ttpt) REVERT: A 244 LEU cc_start: 0.7736 (mm) cc_final: 0.7500 (mp) REVERT: A 263 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7289 (mmmm) REVERT: A 414 LYS cc_start: 0.8203 (tppp) cc_final: 0.8002 (tptm) outliers start: 21 outliers final: 9 residues processed: 79 average time/residue: 0.2669 time to fit residues: 22.2015 Evaluate side-chains 76 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 378 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.0980 chunk 11 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 15 optimal weight: 0.0970 chunk 22 optimal weight: 0.0870 chunk 5 optimal weight: 0.0370 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.0830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.109478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.103478 restraints weight = 5583.143| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.55 r_work: 0.3470 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3139 Z= 0.130 Angle : 0.649 9.929 4281 Z= 0.309 Chirality : 0.045 0.373 537 Planarity : 0.005 0.040 526 Dihedral : 3.952 20.635 440 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.95 % Allowed : 22.29 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.38), residues: 412 helix: 1.82 (0.25), residues: 351 sheet: None (None), residues: 0 loop : 0.16 (0.83), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 397 TYR 0.024 0.002 TYR A 317 PHE 0.024 0.002 PHE A 323 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3139) covalent geometry : angle 0.64939 ( 4281) hydrogen bonds : bond 0.03972 ( 266) hydrogen bonds : angle 4.55563 ( 792) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.086 Fit side-chains REVERT: A 10 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.8193 (t80) REVERT: A 49 LEU cc_start: 0.8448 (tm) cc_final: 0.8211 (tp) REVERT: A 55 LYS cc_start: 0.6074 (OUTLIER) cc_final: 0.4925 (ttpt) REVERT: A 244 LEU cc_start: 0.7645 (mm) cc_final: 0.7427 (mp) REVERT: A 414 LYS cc_start: 0.8074 (tppp) cc_final: 0.7871 (tttm) outliers start: 16 outliers final: 7 residues processed: 76 average time/residue: 0.2796 time to fit residues: 22.3290 Evaluate side-chains 73 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 378 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 chunk 32 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 40 optimal weight: 0.3980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.108650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.102726 restraints weight = 5553.839| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.53 r_work: 0.3458 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3139 Z= 0.155 Angle : 0.637 7.372 4281 Z= 0.308 Chirality : 0.043 0.129 537 Planarity : 0.005 0.040 526 Dihedral : 3.944 20.942 440 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.95 % Allowed : 23.22 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.39), residues: 412 helix: 1.82 (0.25), residues: 351 sheet: None (None), residues: 0 loop : 0.04 (0.82), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 397 TYR 0.022 0.002 TYR A 299 PHE 0.026 0.002 PHE A 323 HIS 0.003 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 3139) covalent geometry : angle 0.63748 ( 4281) hydrogen bonds : bond 0.04045 ( 266) hydrogen bonds : angle 4.58123 ( 792) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.148 Fit side-chains REVERT: A 10 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.8173 (t80) REVERT: A 49 LEU cc_start: 0.8473 (tm) cc_final: 0.8234 (tp) REVERT: A 55 LYS cc_start: 0.6085 (OUTLIER) cc_final: 0.4962 (ttpt) REVERT: A 263 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7227 (mmmm) REVERT: A 414 LYS cc_start: 0.8145 (tppp) cc_final: 0.7921 (tptm) outliers start: 16 outliers final: 8 residues processed: 75 average time/residue: 0.2900 time to fit residues: 22.8651 Evaluate side-chains 75 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 378 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.0980 chunk 37 optimal weight: 0.0970 chunk 4 optimal weight: 0.4980 chunk 7 optimal weight: 0.0770 chunk 28 optimal weight: 0.2980 chunk 40 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.0980 chunk 15 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 overall best weight: 0.0936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.110934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.105003 restraints weight = 5431.032| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.51 r_work: 0.3498 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3139 Z= 0.128 Angle : 0.657 10.430 4281 Z= 0.312 Chirality : 0.044 0.299 537 Planarity : 0.004 0.040 526 Dihedral : 3.926 19.564 440 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.72 % Allowed : 25.08 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.39), residues: 412 helix: 1.87 (0.26), residues: 351 sheet: None (None), residues: 0 loop : 0.14 (0.83), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 397 TYR 0.022 0.002 TYR A 299 PHE 0.024 0.001 PHE A 323 HIS 0.001 0.000 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3139) covalent geometry : angle 0.65665 ( 4281) hydrogen bonds : bond 0.03887 ( 266) hydrogen bonds : angle 4.53902 ( 792) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.156 Fit side-chains REVERT: A 49 LEU cc_start: 0.8395 (tm) cc_final: 0.8181 (tp) REVERT: A 55 LYS cc_start: 0.6102 (OUTLIER) cc_final: 0.4506 (ttpp) REVERT: A 414 LYS cc_start: 0.8031 (tppp) cc_final: 0.7813 (tttm) outliers start: 12 outliers final: 7 residues processed: 79 average time/residue: 0.2714 time to fit residues: 22.5926 Evaluate side-chains 75 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 378 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.0770 chunk 12 optimal weight: 0.0570 chunk 32 optimal weight: 0.2980 chunk 40 optimal weight: 0.2980 chunk 18 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 37 optimal weight: 0.0570 overall best weight: 0.1374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.111947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.105334 restraints weight = 5387.225| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.63 r_work: 0.3499 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3139 Z= 0.135 Angle : 0.670 10.826 4281 Z= 0.319 Chirality : 0.043 0.166 537 Planarity : 0.005 0.041 526 Dihedral : 3.898 19.591 440 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.02 % Allowed : 25.08 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.39), residues: 412 helix: 1.88 (0.26), residues: 352 sheet: None (None), residues: 0 loop : 0.19 (0.83), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 397 TYR 0.022 0.002 TYR A 299 PHE 0.025 0.002 PHE A 323 HIS 0.002 0.000 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 3139) covalent geometry : angle 0.67025 ( 4281) hydrogen bonds : bond 0.03976 ( 266) hydrogen bonds : angle 4.52921 ( 792) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1275.98 seconds wall clock time: 22 minutes 35.55 seconds (1355.55 seconds total)