Starting phenix.real_space_refine on Tue Mar 3 10:50:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggv_40022/03_2026/8ggv_40022.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggv_40022/03_2026/8ggv_40022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ggv_40022/03_2026/8ggv_40022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggv_40022/03_2026/8ggv_40022.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ggv_40022/03_2026/8ggv_40022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggv_40022/03_2026/8ggv_40022.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 13 5.16 5 C 1378 2.51 5 N 331 2.21 5 O 342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2064 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2049 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'TRP:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 4, 'HIS:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 107 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: 0.54, per 1000 atoms: 0.26 Number of scatterers: 2064 At special positions: 0 Unit cell: (55.5328, 82.4315, 62.4744, 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 13 16.00 O 342 8.00 N 331 7.00 C 1378 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: 0.28 Conformation dependent library (CDL) restraints added in 95.1 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: 11 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.634A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 4.105A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 137 Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.928A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.603A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.807A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.950A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.974A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.720A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR R 316 " --> pdb=" O ASN R 312 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 165 hydrogen bonds defined for protein. 495 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: 0.22 Time building geometry restraints manager: 0.35 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: 628 1.34 - 1.46: 449 1.46 - 1.57: 1022 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 2117 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 6.98e+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 5.45e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.565 -0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.438 -0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" CAD G1I R 501 " pdb=" OAK G1I R 501 " ideal model delta sigma weight residual 1.353 1.321 0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 2112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 2736 1.09 - 2.19: 136 2.19 - 3.28: 22 3.28 - 4.38: 8 4.38 - 5.47: 5 Bond angle restraints: 2907 Sorted by residual: angle pdb=" C THR R 96 " pdb=" N LYS R 97 " pdb=" CA LYS R 97 " ideal model delta sigma weight residual 121.54 125.83 -4.29 1.91e+00 2.74e-01 5.03e+00 angle pdb=" C LEU R 95 " pdb=" N THR R 96 " pdb=" CA THR R 96 " ideal model delta sigma weight residual 122.06 118.50 3.56 1.86e+00 2.89e-01 3.65e+00 angle pdb=" C ILE R 159 " pdb=" N VAL R 160 " pdb=" CA VAL R 160 " ideal model delta sigma weight residual 120.42 117.77 2.65 1.42e+00 4.96e-01 3.47e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.10 -5.47 3.00e+00 1.11e-01 3.33e+00 angle pdb=" C SER R 207 " pdb=" N PHE R 208 " pdb=" CA PHE R 208 " ideal model delta sigma weight residual 122.46 119.25 3.21 1.80e+00 3.09e-01 3.17e+00 ... (remaining 2902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 1087 15.90 - 31.79: 88 31.79 - 47.69: 25 47.69 - 63.59: 2 63.59 - 79.48: 2 Dihedral angle restraints: 1204 sinusoidal: 376 harmonic: 828 Sorted by residual: dihedral pdb=" CA GLN R 170 " pdb=" C GLN R 170 " pdb=" N MET R 171 " pdb=" CA MET R 171 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual 180.00 -163.17 -16.83 0 5.00e+00 4.00e-02 1.13e+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 -164.39 -15.61 0 5.00e+00 4.00e-02 9.74e+00 ... (remaining 1201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 223 0.033 - 0.066: 96 0.066 - 0.099: 34 0.099 - 0.131: 2 0.131 - 0.164: 1 Chirality restraints: 356 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 2.56 -0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA TRP R 286 " pdb=" N TRP R 286 " pdb=" C TRP R 286 " pdb=" CB TRP R 286 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.78e-01 chirality pdb=" CA LEU R 167 " pdb=" N LEU R 167 " pdb=" C LEU R 167 " pdb=" CB LEU R 167 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.58e-01 ... (remaining 353 not shown) Planarity restraints: 355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO R 168 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 277 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C ILE R 277 " 0.019 2.00e-02 2.50e+03 pdb=" O ILE R 277 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE R 278 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO R 211 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.015 5.00e-02 4.00e+02 ... (remaining 352 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 504 2.80 - 3.33: 2090 3.33 - 3.85: 3338 3.85 - 4.38: 3268 4.38 - 4.90: 5978 Nonbonded interactions: 15178 Sorted by model distance: nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.276 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.412 3.040 nonbonded pdb=" OD1 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.529 3.040 nonbonded pdb=" OE1 GLU R 62 " pdb=" NH1 ARG R 63 " model vdw 2.546 3.120 nonbonded pdb=" NE1 TRP R 99 " pdb=" O GLY R 102 " model vdw 2.585 3.120 ... (remaining 15173 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: 2.870 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.310 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.000 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 0.053 2117 Z= 0.193 Angle : 0.593 5.473 2907 Z= 0.326 Chirality : 0.039 0.164 356 Planarity : 0.003 0.036 355 Dihedral : 13.635 79.481 666 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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 are not related in a simple way. whole: 2.06 (0.50), residues: 277 helix: 2.36 (0.34), residues: 216 sheet: None (None), residues: 0 loop : -2.56 (0.66), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.005 0.001 TYR R 199 PHE 0.014 0.002 PHE R 336 TRP 0.009 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 2117) covalent geometry : angle 0.59293 ( 2907) hydrogen bonds : bond 0.13097 ( 165) hydrogen bonds : angle 4.83684 ( 495) *********************** 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 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.074 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0385 time to fit residues: 2.1113 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 312 ASN R 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.131065 restraints weight = 3318.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134186 restraints weight = 1609.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136304 restraints weight = 962.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137626 restraints weight = 663.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138747 restraints weight = 508.860| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2117 Z= 0.138 Angle : 0.516 5.076 2907 Z= 0.284 Chirality : 0.039 0.125 356 Planarity : 0.003 0.027 355 Dihedral : 4.917 19.007 311 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.78 % Allowed : 10.81 % Favored : 85.41 % 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 are not related in a simple way. whole: 2.38 (0.49), residues: 277 helix: 2.52 (0.33), residues: 218 sheet: None (None), residues: 0 loop : -2.29 (0.69), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.008 0.001 TYR R 326 PHE 0.012 0.001 PHE R 166 TRP 0.008 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 2117) covalent geometry : angle 0.51625 ( 2907) hydrogen bonds : bond 0.05900 ( 165) hydrogen bonds : angle 3.84019 ( 495) *********************** 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 46 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.074 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.0325 time to fit residues: 1.7200 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN R 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.140376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126254 restraints weight = 3392.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.129221 restraints weight = 1664.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.131369 restraints weight = 1009.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132712 restraints weight = 693.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133690 restraints weight = 531.670| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2117 Z= 0.155 Angle : 0.539 5.636 2907 Z= 0.291 Chirality : 0.039 0.121 356 Planarity : 0.003 0.027 355 Dihedral : 4.774 20.178 311 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.95 % Allowed : 16.22 % Favored : 77.84 % 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 are not related in a simple way. whole: 2.48 (0.51), residues: 277 helix: 2.61 (0.33), residues: 221 sheet: None (None), residues: 0 loop : -2.65 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 175 TYR 0.008 0.001 TYR R 326 PHE 0.009 0.001 PHE R 282 TRP 0.009 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 2117) covalent geometry : angle 0.53869 ( 2907) hydrogen bonds : bond 0.06311 ( 165) hydrogen bonds : angle 3.81868 ( 495) *********************** 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 46 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.068 Fit side-chains REVERT: R 309 ILE cc_start: 0.8653 (mm) cc_final: 0.8153 (pt) outliers start: 11 outliers final: 10 residues processed: 38 average time/residue: 0.0373 time to fit residues: 1.8242 Evaluate side-chains 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 318 ASN Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain R residue 332 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.142416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128223 restraints weight = 3360.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.131226 restraints weight = 1654.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133367 restraints weight = 1008.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134693 restraints weight = 701.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135692 restraints weight = 541.216| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2117 Z= 0.134 Angle : 0.503 5.576 2907 Z= 0.274 Chirality : 0.038 0.122 356 Planarity : 0.003 0.027 355 Dihedral : 4.661 19.933 311 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 6.49 % Allowed : 17.30 % Favored : 76.22 % 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 are not related in a simple way. whole: 2.51 (0.50), residues: 277 helix: 2.65 (0.33), residues: 221 sheet: None (None), residues: 0 loop : -2.72 (0.70), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.007 0.001 TYR R 326 PHE 0.008 0.001 PHE R 282 TRP 0.007 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 2117) covalent geometry : angle 0.50280 ( 2907) hydrogen bonds : bond 0.05911 ( 165) hydrogen bonds : angle 3.73064 ( 495) *********************** 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 48 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.045 Fit side-chains REVERT: R 309 ILE cc_start: 0.8647 (mm) cc_final: 0.8080 (pt) outliers start: 12 outliers final: 11 residues processed: 40 average time/residue: 0.0367 time to fit residues: 1.8821 Evaluate side-chains 47 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain R residue 332 PHE 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 6 optimal weight: 0.0470 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.0060 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.145888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.131866 restraints weight = 3349.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134916 restraints weight = 1651.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137099 restraints weight = 1010.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138445 restraints weight = 696.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139418 restraints weight = 533.373| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2117 Z= 0.120 Angle : 0.462 5.041 2907 Z= 0.254 Chirality : 0.038 0.118 356 Planarity : 0.003 0.025 355 Dihedral : 4.459 18.443 311 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 5.95 % Allowed : 20.00 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.50), residues: 277 helix: 2.75 (0.33), residues: 221 sheet: None (None), residues: 0 loop : -2.57 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.006 0.001 TYR R 326 PHE 0.008 0.001 PHE R 282 TRP 0.007 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 2117) covalent geometry : angle 0.46166 ( 2907) hydrogen bonds : bond 0.05250 ( 165) hydrogen bonds : angle 3.57783 ( 495) *********************** 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 49 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.071 Fit side-chains REVERT: R 309 ILE cc_start: 0.8651 (mm) cc_final: 0.8089 (pt) outliers start: 11 outliers final: 9 residues processed: 41 average time/residue: 0.0389 time to fit residues: 2.0354 Evaluate side-chains 47 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain R residue 332 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 0.0470 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 0.0010 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 overall best weight: 0.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN R 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.149766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136047 restraints weight = 3214.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139120 restraints weight = 1583.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141269 restraints weight = 957.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142697 restraints weight = 654.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.143651 restraints weight = 495.254| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2117 Z= 0.107 Angle : 0.446 4.854 2907 Z= 0.243 Chirality : 0.037 0.112 356 Planarity : 0.003 0.024 355 Dihedral : 4.226 17.645 311 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 5.95 % Allowed : 20.54 % Favored : 73.51 % 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 are not related in a simple way. whole: 2.86 (0.51), residues: 277 helix: 2.87 (0.33), residues: 221 sheet: None (None), residues: 0 loop : -2.47 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG R 63 TYR 0.005 0.001 TYR R 326 PHE 0.006 0.001 PHE R 282 TRP 0.006 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 2117) covalent geometry : angle 0.44584 ( 2907) hydrogen bonds : bond 0.04491 ( 165) hydrogen bonds : angle 3.46553 ( 495) *********************** 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 48 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.090 Fit side-chains REVERT: R 318 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8352 (t0) outliers start: 11 outliers final: 6 residues processed: 40 average time/residue: 0.0394 time to fit residues: 2.0148 Evaluate side-chains 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 318 ASN Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 24 optimal weight: 0.4980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN R 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.133589 restraints weight = 3222.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136663 restraints weight = 1576.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138883 restraints weight = 952.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.140357 restraints weight = 650.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.141288 restraints weight = 492.101| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2117 Z= 0.114 Angle : 0.453 4.954 2907 Z= 0.247 Chirality : 0.037 0.112 356 Planarity : 0.003 0.024 355 Dihedral : 4.242 17.676 311 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.78 % Allowed : 23.24 % Favored : 72.97 % 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 are not related in a simple way. whole: 2.90 (0.51), residues: 277 helix: 2.90 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -2.50 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.004 0.001 TYR R 199 PHE 0.007 0.001 PHE R 282 TRP 0.006 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 2117) covalent geometry : angle 0.45309 ( 2907) hydrogen bonds : bond 0.04727 ( 165) hydrogen bonds : angle 3.48579 ( 495) *********************** 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: 7 poor density : 34 time to evaluate : 0.071 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 36 average time/residue: 0.0381 time to fit residues: 1.8048 Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 0.6980 chunk 5 optimal weight: 0.0000 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.146132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132036 restraints weight = 3185.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.135116 restraints weight = 1564.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137329 restraints weight = 944.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.138758 restraints weight = 649.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.139669 restraints weight = 494.077| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2117 Z= 0.131 Angle : 0.487 4.944 2907 Z= 0.264 Chirality : 0.038 0.111 356 Planarity : 0.003 0.024 355 Dihedral : 4.401 18.200 311 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 5.41 % Allowed : 22.16 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.51), residues: 277 helix: 3.03 (0.34), residues: 215 sheet: None (None), residues: 0 loop : -2.54 (0.71), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.006 0.001 TYR R 199 PHE 0.009 0.001 PHE R 282 TRP 0.005 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 2117) covalent geometry : angle 0.48730 ( 2907) hydrogen bonds : bond 0.05436 ( 165) hydrogen bonds : angle 3.58939 ( 495) *********************** 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 46 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.074 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 41 average time/residue: 0.0362 time to fit residues: 1.9318 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 : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 0.0070 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.145652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.131676 restraints weight = 3278.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.134717 restraints weight = 1616.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.136835 restraints weight = 981.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138233 restraints weight = 677.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.139251 restraints weight = 519.617| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2117 Z= 0.129 Angle : 0.498 5.617 2907 Z= 0.266 Chirality : 0.038 0.112 356 Planarity : 0.003 0.024 355 Dihedral : 4.400 18.278 311 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.86 % Allowed : 23.78 % Favored : 71.35 % 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 are not related in a simple way. whole: 2.85 (0.51), residues: 277 helix: 2.88 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -2.57 (0.70), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.005 0.001 TYR R 199 PHE 0.008 0.001 PHE R 282 TRP 0.006 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 2117) covalent geometry : angle 0.49812 ( 2907) hydrogen bonds : bond 0.05376 ( 165) hydrogen bonds : angle 3.58979 ( 495) *********************** 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 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.043 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 38 average time/residue: 0.0358 time to fit residues: 1.7570 Evaluate side-chains 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.130147 restraints weight = 3386.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.133147 restraints weight = 1659.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135358 restraints weight = 1001.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.136751 restraints weight = 687.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137767 restraints weight = 520.277| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2117 Z= 0.128 Angle : 0.502 5.912 2907 Z= 0.269 Chirality : 0.038 0.113 356 Planarity : 0.003 0.024 355 Dihedral : 4.406 18.091 311 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.86 % Allowed : 23.78 % Favored : 71.35 % 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 are not related in a simple way. whole: 2.82 (0.51), residues: 277 helix: 2.86 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -2.60 (0.70), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.005 0.001 TYR R 199 PHE 0.007 0.001 PHE R 282 TRP 0.006 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 2117) covalent geometry : angle 0.50240 ( 2907) hydrogen bonds : bond 0.05343 ( 165) hydrogen bonds : angle 3.56060 ( 495) ********************** 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 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.055 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 39 average time/residue: 0.0364 time to fit residues: 1.8006 Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 15 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.0370 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.0170 chunk 26 optimal weight: 0.0570 chunk 8 optimal weight: 0.5980 overall best weight: 0.1614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.151027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137012 restraints weight = 3347.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140158 restraints weight = 1626.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142470 restraints weight = 979.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.143938 restraints weight = 663.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.144966 restraints weight = 499.061| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2117 Z= 0.105 Angle : 0.473 5.867 2907 Z= 0.247 Chirality : 0.037 0.110 356 Planarity : 0.003 0.023 355 Dihedral : 4.166 17.318 311 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.70 % Allowed : 26.49 % Favored : 70.81 % 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 are not related in a simple way. whole: 2.83 (0.51), residues: 277 helix: 2.89 (0.34), residues: 220 sheet: None (None), residues: 0 loop : -2.58 (0.69), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 304 TYR 0.005 0.001 TYR R 308 PHE 0.008 0.001 PHE R 321 TRP 0.008 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 2117) covalent geometry : angle 0.47275 ( 2907) hydrogen bonds : bond 0.03957 ( 165) hydrogen bonds : angle 3.42692 ( 495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 596.75 seconds wall clock time: 10 minutes 46.93 seconds (646.93 seconds total)