Starting phenix.real_space_refine on Thu Oct 22 18:01:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26qs_80832/10_2026/26qs_80832.cif Found real_map, /net/cci-nas-00/data/ceres_data/26qs_80832/10_2026/26qs_80832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/26qs_80832/10_2026/26qs_80832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26qs_80832/10_2026/26qs_80832.map" model { file = "/net/cci-nas-00/data/ceres_data/26qs_80832/10_2026/26qs_80832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26qs_80832/10_2026/26qs_80832.cif" } resolution = 2.88 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= 0.093 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 28 5.16 5 C 2059 2.51 5 N 518 2.21 5 O 557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3164 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3128 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 375} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'UPG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.81, per 1000 atoms: 0.26 Number of scatterers: 3164 At special positions: 0 Unit cell: (73, 60.59, 80.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 2 15.00 O 557 8.00 N 518 7.00 C 2059 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 323 " distance=2.04 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: 0.26 Conformation dependent library (CDL) restraints added in 115.4 milliseconds 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 728 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 3 sheets defined 60.6% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 1 through 36 Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.530A pdb=" N LEU A 50 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 92 through 105 removed outlier: 3.918A pdb=" N ASP A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 Proline residue: A 130 - end of helix removed outlier: 3.604A pdb=" N VAL A 134 " --> pdb=" O PRO A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 removed outlier: 3.612A pdb=" N ASP A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 204 removed outlier: 5.668A pdb=" N HIS A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 217 through 223 Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.682A pdb=" N ALA A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 224 through 229' Processing helix chain 'A' and resid 234 through 246 removed outlier: 3.516A pdb=" N PHE A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.607A pdb=" N ILE A 288 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 289 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 294 Processing helix chain 'A' and resid 295 through 311 Processing helix chain 'A' and resid 314 through 339 Processing helix chain 'A' and resid 345 through 368 Processing sheet with id=AA1, first strand: chain 'A' and resid 110 through 114 removed outlier: 8.846A pdb=" N ARG A 111 " --> pdb=" O TYR A 81 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL A 83 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE A 113 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU A 85 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 53 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU A 84 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 55 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N CYS A 86 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS A 57 " --> pdb=" O CYS A 86 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N CYS A 143 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLY A 166 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG A 249 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 167 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 148 removed outlier: 4.054A pdb=" N MET A 258 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR A 173 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 374 through 375 174 hydrogen bonds defined for protein. 510 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: 0.52 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: 1.18 - 1.31: 490 1.31 - 1.44: 916 1.44 - 1.56: 1792 1.56 - 1.69: 6 1.69 - 1.81: 45 Bond restraints: 3249 Sorted by residual: bond pdb=" C2C UPG A 401 " pdb=" C3C UPG A 401 " ideal model delta sigma weight residual 1.531 1.266 0.265 2.00e-02 2.50e+03 1.76e+02 bond pdb=" C2 UPG A 401 " pdb=" N3 UPG A 401 " ideal model delta sigma weight residual 1.371 1.546 -0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" C1C UPG A 401 " pdb=" C2C UPG A 401 " ideal model delta sigma weight residual 1.529 1.674 -0.145 2.00e-02 2.50e+03 5.29e+01 bond pdb=" C2 UPG A 401 " pdb=" N1 UPG A 401 " ideal model delta sigma weight residual 1.382 1.521 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C4C UPG A 401 " pdb=" C5C UPG A 401 " ideal model delta sigma weight residual 1.514 1.381 0.133 2.00e-02 2.50e+03 4.44e+01 ... (remaining 3244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 4369 2.56 - 5.12: 31 5.12 - 7.67: 7 7.67 - 10.23: 1 10.23 - 12.79: 3 Bond angle restraints: 4411 Sorted by residual: angle pdb=" O1B UPG A 401 " pdb=" PB UPG A 401 " pdb=" O2B UPG A 401 " ideal model delta sigma weight residual 122.19 109.40 12.79 3.00e+00 1.11e-01 1.82e+01 angle pdb=" O1A UPG A 401 " pdb=" PA UPG A 401 " pdb=" O2A UPG A 401 " ideal model delta sigma weight residual 121.98 109.50 12.48 3.00e+00 1.11e-01 1.73e+01 angle pdb=" O3A UPG A 401 " pdb=" PB UPG A 401 " pdb=" O3B UPG A 401 " ideal model delta sigma weight residual 97.80 109.72 -11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O3A UPG A 401 " pdb=" PA UPG A 401 " pdb=" O5C UPG A 401 " ideal model delta sigma weight residual 100.87 109.23 -8.36 3.00e+00 1.11e-01 7.76e+00 angle pdb=" N ILE A 293 " pdb=" CA ILE A 293 " pdb=" C ILE A 293 " ideal model delta sigma weight residual 112.98 109.59 3.39 1.25e+00 6.40e-01 7.36e+00 ... (remaining 4406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.97: 1821 23.97 - 47.94: 92 47.94 - 71.90: 14 71.90 - 95.87: 10 95.87 - 119.84: 2 Dihedral angle restraints: 1939 sinusoidal: 803 harmonic: 1136 Sorted by residual: dihedral pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " pdb=" SG CYS A 323 " pdb=" CB CYS A 323 " ideal model delta sinusoidal sigma weight residual -86.00 -164.78 78.78 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" C2' UPG A 401 " pdb=" C1' UPG A 401 " pdb=" O5' UPG A 401 " pdb=" C5' UPG A 401 " ideal model delta sinusoidal sigma weight residual -59.18 60.66 -119.84 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C5' UPG A 401 " pdb=" C1' UPG A 401 " pdb=" O5' UPG A 401 " pdb=" O3B UPG A 401 " ideal model delta sinusoidal sigma weight residual 298.15 178.40 119.75 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 1936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 449 0.070 - 0.141: 37 0.141 - 0.211: 0 0.211 - 0.281: 1 0.281 - 0.352: 1 Chirality restraints: 488 Sorted by residual: chirality pdb=" C3C UPG A 401 " pdb=" C2C UPG A 401 " pdb=" C4C UPG A 401 " pdb=" O3C UPG A 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C4C UPG A 401 " pdb=" C3C UPG A 401 " pdb=" C5C UPG A 401 " pdb=" O4C UPG A 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.67 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C1' UPG A 401 " pdb=" C2' UPG A 401 " pdb=" O3B UPG A 401 " pdb=" O5' UPG A 401 " both_signs ideal model delta sigma weight residual False -2.23 -2.35 0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 485 not shown) Planarity restraints: 543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 63 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO A 64 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 150 " -0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO A 151 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 151 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 151 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 92 " -0.015 5.00e-02 4.00e+02 2.23e-02 7.94e-01 pdb=" N PRO A 93 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.012 5.00e-02 4.00e+02 ... (remaining 540 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 721 2.79 - 3.32: 2936 3.32 - 3.84: 5444 3.84 - 4.37: 5940 4.37 - 4.90: 10704 Nonbonded interactions: 25745 Sorted by model distance: nonbonded pdb=" O GLN A 178 " pdb=" OH TYR A 264 " model vdw 2.259 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" O SER A 261 " model vdw 2.346 3.120 nonbonded pdb=" NE2 GLN A 45 " pdb=" O LYS A 49 " model vdw 2.351 3.120 nonbonded pdb=" O2C UPG A 401 " pdb=" O3C UPG A 401 " model vdw 2.364 2.432 nonbonded pdb=" O PRO A 58 " pdb=" O3C UPG A 401 " model vdw 2.379 3.040 ... (remaining 25740 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.360 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:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 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 : 0.009 0.265 3250 Z= 0.453 Angle : 0.645 12.791 4413 Z= 0.299 Chirality : 0.042 0.352 488 Planarity : 0.003 0.028 543 Dihedral : 16.018 119.841 1208 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.10 % Allowed : 16.52 % Favored : 81.38 % 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: -1.01 (0.38), residues: 389 helix: 0.40 (0.32), residues: 216 sheet: -0.42 (0.83), residues: 39 loop : -2.53 (0.43), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 379 TYR 0.007 0.001 TYR A 188 PHE 0.010 0.001 PHE A 19 TRP 0.006 0.000 TRP A 23 HIS 0.001 0.000 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00900 / 0.45 ( 3249) covalent geometry : angle 0.64451 / 0.30 ( 4411) SS BOND : bond 0.00506 / 0.27 ( 1) SS BOND : angle 0.73461 / 0.39 ( 2) hydrogen bonds : bond 0.13631 / 8.70 ( 174) hydrogen bonds : angle 5.15294 / 3.73 ( 510) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.118 Fit side-chains REVERT: A 63 ASP cc_start: 0.7476 (p0) cc_final: 0.6978 (p0) REVERT: A 66 LEU cc_start: 0.7099 (tt) cc_final: 0.6880 (tp) REVERT: A 82 GLU cc_start: 0.8118 (pt0) cc_final: 0.7391 (pt0) REVERT: A 113 PHE cc_start: 0.6935 (m-80) cc_final: 0.6536 (m-80) REVERT: A 129 MET cc_start: 0.7563 (mmm) cc_final: 0.7363 (mmm) REVERT: A 178 GLN cc_start: 0.7370 (tp40) cc_final: 0.7041 (mp10) REVERT: A 185 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7304 (mt-10) REVERT: A 255 GLN cc_start: 0.8257 (mt0) cc_final: 0.7988 (mt0) outliers start: 7 outliers final: 0 residues processed: 94 average time/residue: 0.5159 time to fit residues: 49.7826 Evaluate side-chains 52 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37] chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 88 GLN A 160 GLN ** A 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 GLN A 260 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.173978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139184 restraints weight = 3615.736| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.95 r_work: 0.3403 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3250 Z= 0.147 Angle : 0.571 5.471 4413 Z= 0.291 Chirality : 0.044 0.231 488 Planarity : 0.004 0.040 543 Dihedral : 6.100 41.632 480 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.71 % Allowed : 19.52 % Favored : 74.77 % 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: 0.11 (0.40), residues: 389 helix: 1.25 (0.34), residues: 221 sheet: 0.44 (0.88), residues: 35 loop : -2.12 (0.44), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 195 TYR 0.010 0.001 TYR A 349 PHE 0.014 0.002 PHE A 327 TRP 0.018 0.001 TRP A 23 HIS 0.006 0.002 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 3249) covalent geometry : angle 0.56734 / 0.29 ( 4411) SS BOND : bond 0.01747 / 0.92 ( 1) SS BOND : angle 3.00976 / 1.65 ( 2) hydrogen bonds : bond 0.04761 / 3.06 ( 174) hydrogen bonds : angle 4.04763 / 2.87 ( 510) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.138 Fit side-chains REVERT: A 63 ASP cc_start: 0.7427 (p0) cc_final: 0.6791 (p0) REVERT: A 65 ASN cc_start: 0.8539 (m-40) cc_final: 0.7873 (m110) REVERT: A 78 TYR cc_start: 0.8786 (t80) cc_final: 0.7909 (t80) REVERT: A 82 GLU cc_start: 0.8710 (pt0) cc_final: 0.7910 (pt0) REVERT: A 107 ASN cc_start: 0.7612 (m-40) cc_final: 0.7104 (t0) REVERT: A 138 ASP cc_start: 0.7731 (m-30) cc_final: 0.6848 (p0) REVERT: A 185 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7963 (mt-10) REVERT: A 211 MET cc_start: 0.8138 (mtp) cc_final: 0.7775 (ttm) REVERT: A 235 GLU cc_start: 0.7991 (pm20) cc_final: 0.7074 (pm20) REVERT: A 255 GLN cc_start: 0.8764 (mt0) cc_final: 0.8439 (mt0) REVERT: A 294 SER cc_start: 0.8445 (m) cc_final: 0.8194 (p) REVERT: A 365 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7636 (mt) outliers start: 19 outliers final: 1 residues processed: 82 average time/residue: 0.4660 time to fit residues: 39.4302 Evaluate side-chains 64 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 365 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: [4, 14, 9, 25, 32, 20, 2, 24, 36, 7, 33] chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 7 optimal weight: 0.0870 chunk 33 optimal weight: 0.4980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A 201 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.172848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.138201 restraints weight = 3639.811| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.97 r_work: 0.3455 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3250 Z= 0.110 Angle : 0.485 5.074 4413 Z= 0.251 Chirality : 0.041 0.203 488 Planarity : 0.004 0.040 543 Dihedral : 5.184 43.241 480 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.60 % Allowed : 23.72 % Favored : 72.67 % 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: 0.73 (0.42), residues: 389 helix: 1.78 (0.35), residues: 221 sheet: 0.70 (0.89), residues: 35 loop : -1.90 (0.45), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.008 0.001 TYR A 188 PHE 0.012 0.001 PHE A 327 TRP 0.013 0.001 TRP A 23 HIS 0.003 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 3249) covalent geometry : angle 0.48405 / 0.25 ( 4411) SS BOND : bond 0.00634 / 0.33 ( 1) SS BOND : angle 1.76253 / 0.93 ( 2) hydrogen bonds : bond 0.04103 / 2.64 ( 174) hydrogen bonds : angle 3.76928 / 2.65 ( 510) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.121 Fit side-chains REVERT: A 1 MET cc_start: 0.4789 (OUTLIER) cc_final: 0.3328 (mmp) REVERT: A 20 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8603 (mp) REVERT: A 63 ASP cc_start: 0.7365 (p0) cc_final: 0.6806 (p0) REVERT: A 65 ASN cc_start: 0.8457 (m-40) cc_final: 0.7871 (m110) REVERT: A 78 TYR cc_start: 0.8764 (t80) cc_final: 0.7863 (t80) REVERT: A 107 ASN cc_start: 0.7592 (m-40) cc_final: 0.7082 (t0) REVERT: A 138 ASP cc_start: 0.7626 (m-30) cc_final: 0.6844 (p0) REVERT: A 185 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7936 (mt-10) REVERT: A 211 MET cc_start: 0.8110 (mtp) cc_final: 0.7824 (ttm) REVERT: A 235 GLU cc_start: 0.8031 (pm20) cc_final: 0.7197 (pm20) REVERT: A 255 GLN cc_start: 0.8780 (mt0) cc_final: 0.8444 (mt0) REVERT: A 373 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7604 (mp) outliers start: 12 outliers final: 4 residues processed: 65 average time/residue: 0.4635 time to fit residues: 31.1543 Evaluate side-chains 62 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 387 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: [12, 35, 2, 24, 9, 31, 36, 8, 3, 19, 37] chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.0470 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS A 201 ASN A 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.160564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124805 restraints weight = 3578.505| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.92 r_work: 0.3296 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3250 Z= 0.138 Angle : 0.513 5.260 4413 Z= 0.269 Chirality : 0.041 0.170 488 Planarity : 0.004 0.042 543 Dihedral : 5.117 43.664 480 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.60 % Allowed : 25.23 % Favored : 71.17 % 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: 0.89 (0.42), residues: 389 helix: 1.99 (0.35), residues: 215 sheet: 0.85 (0.88), residues: 35 loop : -1.83 (0.45), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 148 TYR 0.009 0.001 TYR A 349 PHE 0.014 0.002 PHE A 327 TRP 0.014 0.001 TRP A 23 HIS 0.004 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 3249) covalent geometry : angle 0.51147 / 0.27 ( 4411) SS BOND : bond 0.00948 / 0.50 ( 1) SS BOND : angle 1.98356 / 1.06 ( 2) hydrogen bonds : bond 0.04545 / 2.92 ( 174) hydrogen bonds : angle 3.86553 / 2.68 ( 510) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.138 Fit side-chains REVERT: A 1 MET cc_start: 0.4721 (OUTLIER) cc_final: 0.3337 (mmp) REVERT: A 63 ASP cc_start: 0.7305 (p0) cc_final: 0.6752 (p0) REVERT: A 65 ASN cc_start: 0.8526 (m-40) cc_final: 0.7922 (m110) REVERT: A 78 TYR cc_start: 0.8804 (t80) cc_final: 0.7980 (t80) REVERT: A 82 GLU cc_start: 0.8844 (pt0) cc_final: 0.8581 (pt0) REVERT: A 107 ASN cc_start: 0.7851 (m-40) cc_final: 0.7261 (t0) REVERT: A 138 ASP cc_start: 0.7565 (m-30) cc_final: 0.6791 (p0) REVERT: A 185 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7861 (mt-10) REVERT: A 211 MET cc_start: 0.8114 (mtp) cc_final: 0.7769 (ttm) REVERT: A 235 GLU cc_start: 0.7903 (pm20) cc_final: 0.7085 (pm20) REVERT: A 255 GLN cc_start: 0.8785 (mt0) cc_final: 0.8358 (mt0) REVERT: A 284 LEU cc_start: 0.7397 (mt) cc_final: 0.7183 (OUTLIER) REVERT: A 365 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7831 (mt) REVERT: A 373 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7666 (mp) outliers start: 12 outliers final: 6 residues processed: 68 average time/residue: 0.4400 time to fit residues: 30.9162 Evaluate side-chains 62 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 387 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: [7, 14, 8, 5, 17, 28, 30, 22, 0, 9, 12] chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.161252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125947 restraints weight = 3617.053| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.96 r_work: 0.3220 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3250 Z= 0.222 Angle : 0.621 7.334 4413 Z= 0.328 Chirality : 0.045 0.221 488 Planarity : 0.004 0.043 543 Dihedral : 5.652 48.562 480 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.50 % Allowed : 24.62 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.64 (0.41), residues: 389 helix: 1.73 (0.35), residues: 212 sheet: 0.85 (0.88), residues: 35 loop : -1.81 (0.43), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 148 TYR 0.011 0.001 TYR A 349 PHE 0.017 0.002 PHE A 327 TRP 0.016 0.002 TRP A 23 HIS 0.006 0.002 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 ( 3249) covalent geometry : angle 0.60936 / 0.32 ( 4411) SS BOND : bond 0.02373 / 1.25 ( 1) SS BOND : angle 5.74090 / 3.09 ( 2) hydrogen bonds : bond 0.05529 / 3.59 ( 174) hydrogen bonds : angle 4.19737 / 2.95 ( 510) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.119 Fit side-chains REVERT: A 1 MET cc_start: 0.4782 (OUTLIER) cc_final: 0.3281 (mmp) REVERT: A 63 ASP cc_start: 0.7574 (p0) cc_final: 0.7011 (p0) REVERT: A 82 GLU cc_start: 0.8771 (pt0) cc_final: 0.8474 (pt0) REVERT: A 107 ASN cc_start: 0.8134 (m-40) cc_final: 0.7470 (t0) REVERT: A 138 ASP cc_start: 0.7698 (m-30) cc_final: 0.6938 (p0) REVERT: A 211 MET cc_start: 0.8282 (mtp) cc_final: 0.7914 (ttm) REVERT: A 235 GLU cc_start: 0.7889 (pm20) cc_final: 0.7138 (pm20) REVERT: A 255 GLN cc_start: 0.8914 (mt0) cc_final: 0.8657 (mt0) REVERT: A 283 MET cc_start: 0.7616 (mtp) cc_final: 0.7300 (mmt) REVERT: A 284 LEU cc_start: 0.7359 (mt) cc_final: 0.7151 (OUTLIER) REVERT: A 365 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8164 (mt) REVERT: A 387 THR cc_start: 0.6593 (OUTLIER) cc_final: 0.6159 (p) outliers start: 15 outliers final: 5 residues processed: 70 average time/residue: 0.4146 time to fit residues: 30.0124 Evaluate side-chains 63 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 387 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: [24, 33, 37, 12, 36, 21, 27, 29, 17, 25, 30] chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 25 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.157448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.121985 restraints weight = 3601.969| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.94 r_work: 0.3254 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3250 Z= 0.134 Angle : 0.525 5.212 4413 Z= 0.278 Chirality : 0.041 0.155 488 Planarity : 0.004 0.042 543 Dihedral : 5.065 47.897 480 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.80 % Allowed : 25.23 % Favored : 69.97 % 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: 1.03 (0.41), residues: 389 helix: 1.98 (0.35), residues: 212 sheet: 1.53 (0.98), residues: 27 loop : -1.49 (0.44), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 148 TYR 0.012 0.001 TYR A 132 PHE 0.017 0.001 PHE A 327 TRP 0.015 0.001 TRP A 23 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 3249) covalent geometry : angle 0.52007 / 0.28 ( 4411) SS BOND : bond 0.01285 / 0.68 ( 1) SS BOND : angle 3.45665 / 1.85 ( 2) hydrogen bonds : bond 0.04753 / 3.10 ( 174) hydrogen bonds : angle 3.96212 / 2.77 ( 510) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.087 Fit side-chains REVERT: A 1 MET cc_start: 0.4771 (OUTLIER) cc_final: 0.3366 (mmp) REVERT: A 20 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8663 (mp) REVERT: A 63 ASP cc_start: 0.7327 (p0) cc_final: 0.6847 (p0) REVERT: A 65 ASN cc_start: 0.8507 (m-40) cc_final: 0.7932 (m110) REVERT: A 82 GLU cc_start: 0.8769 (pt0) cc_final: 0.8507 (pt0) REVERT: A 107 ASN cc_start: 0.8139 (m-40) cc_final: 0.7451 (t0) REVERT: A 138 ASP cc_start: 0.7659 (m-30) cc_final: 0.6852 (p0) REVERT: A 178 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: A 211 MET cc_start: 0.8081 (mtp) cc_final: 0.7831 (ttm) REVERT: A 235 GLU cc_start: 0.7874 (pm20) cc_final: 0.7090 (pm20) REVERT: A 255 GLN cc_start: 0.8819 (mt0) cc_final: 0.8590 (mt0) REVERT: A 283 MET cc_start: 0.7599 (mtp) cc_final: 0.7318 (mmt) REVERT: A 284 LEU cc_start: 0.7376 (mt) cc_final: 0.7175 (OUTLIER) REVERT: A 365 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8033 (mt) REVERT: A 373 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7851 (mp) REVERT: A 387 THR cc_start: 0.6484 (OUTLIER) cc_final: 0.6054 (p) outliers start: 16 outliers final: 5 residues processed: 69 average time/residue: 0.4094 time to fit residues: 29.2211 Evaluate side-chains 63 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 387 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: [14, 29, 34, 37, 16, 1, 19, 26, 24, 22, 0] chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 0.0370 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN A 201 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.153361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.117491 restraints weight = 3723.119| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.03 r_work: 0.3210 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3250 Z= 0.198 Angle : 0.589 6.437 4413 Z= 0.309 Chirality : 0.043 0.143 488 Planarity : 0.004 0.042 543 Dihedral : 5.368 48.895 480 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.50 % Allowed : 27.33 % Favored : 68.17 % 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: 0.76 (0.41), residues: 389 helix: 1.78 (0.35), residues: 212 sheet: 1.03 (0.86), residues: 35 loop : -1.69 (0.44), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 148 TYR 0.016 0.001 TYR A 132 PHE 0.017 0.002 PHE A 327 TRP 0.017 0.002 TRP A 23 HIS 0.004 0.002 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 ( 3249) covalent geometry : angle 0.58532 / 0.31 ( 4411) SS BOND : bond 0.01344 / 0.71 ( 1) SS BOND : angle 3.04143 / 1.60 ( 2) hydrogen bonds : bond 0.05286 / 3.41 ( 174) hydrogen bonds : angle 4.10532 / 2.85 ( 510) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.148 Fit side-chains REVERT: A 1 MET cc_start: 0.4792 (OUTLIER) cc_final: 0.3385 (mmp) REVERT: A 63 ASP cc_start: 0.7437 (p0) cc_final: 0.6759 (p0) REVERT: A 82 GLU cc_start: 0.8771 (pt0) cc_final: 0.8484 (pt0) REVERT: A 107 ASN cc_start: 0.8200 (m-40) cc_final: 0.7511 (t0) REVERT: A 138 ASP cc_start: 0.7720 (m-30) cc_final: 0.6947 (p0) REVERT: A 178 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7843 (mp10) REVERT: A 211 MET cc_start: 0.8226 (mtp) cc_final: 0.7849 (ttm) REVERT: A 235 GLU cc_start: 0.7901 (pm20) cc_final: 0.7131 (pm20) REVERT: A 283 MET cc_start: 0.7619 (mtp) cc_final: 0.7303 (mmt) REVERT: A 284 LEU cc_start: 0.7381 (mt) cc_final: 0.7174 (OUTLIER) REVERT: A 373 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7914 (mp) outliers start: 15 outliers final: 8 residues processed: 61 average time/residue: 0.4526 time to fit residues: 28.5527 Evaluate side-chains 61 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 373 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: [22, 20, 23, 24, 35, 13, 9, 27, 29, 31, 32] chunk 22 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 GLN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.164105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.128349 restraints weight = 3691.685| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.02 r_work: 0.3249 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3250 Z= 0.142 Angle : 0.549 9.177 4413 Z= 0.285 Chirality : 0.041 0.141 488 Planarity : 0.004 0.041 543 Dihedral : 5.104 48.614 480 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.50 % Allowed : 27.03 % Favored : 68.47 % 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: 0.98 (0.41), residues: 389 helix: 1.87 (0.35), residues: 214 sheet: 1.37 (0.94), residues: 27 loop : -1.40 (0.45), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 148 TYR 0.014 0.001 TYR A 132 PHE 0.018 0.002 PHE A 327 TRP 0.016 0.001 TRP A 23 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 3249) covalent geometry : angle 0.54682 / 0.28 ( 4411) SS BOND : bond 0.01079 / 0.57 ( 1) SS BOND : angle 2.56375 / 1.35 ( 2) hydrogen bonds : bond 0.04864 / 3.17 ( 174) hydrogen bonds : angle 4.02619 / 2.83 ( 510) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.094 Fit side-chains REVERT: A 1 MET cc_start: 0.4861 (OUTLIER) cc_final: 0.3572 (mmp) REVERT: A 20 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8658 (mp) REVERT: A 63 ASP cc_start: 0.7358 (p0) cc_final: 0.6804 (p0) REVERT: A 82 GLU cc_start: 0.8784 (pt0) cc_final: 0.8530 (pt0) REVERT: A 107 ASN cc_start: 0.8206 (m-40) cc_final: 0.7505 (t0) REVERT: A 138 ASP cc_start: 0.7700 (m-30) cc_final: 0.6967 (p0) REVERT: A 140 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8192 (mp) REVERT: A 145 SER cc_start: 0.8936 (t) cc_final: 0.8693 (m) REVERT: A 161 MET cc_start: 0.8203 (tpp) cc_final: 0.7711 (mmt) REVERT: A 178 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7843 (mp10) REVERT: A 211 MET cc_start: 0.8197 (mtp) cc_final: 0.7802 (ttm) REVERT: A 235 GLU cc_start: 0.7887 (pm20) cc_final: 0.7074 (pm20) REVERT: A 283 MET cc_start: 0.7592 (mtp) cc_final: 0.7345 (mmt) REVERT: A 284 LEU cc_start: 0.7413 (mt) cc_final: 0.7206 (OUTLIER) REVERT: A 373 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7830 (mp) outliers start: 15 outliers final: 6 residues processed: 61 average time/residue: 0.4363 time to fit residues: 27.5578 Evaluate side-chains 61 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 373 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: [11, 13, 27, 32, 35, 4, 18, 17, 37, 12, 0] chunk 11 optimal weight: 0.0020 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 0.0370 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 overall best weight: 0.4466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 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 = 0.3765 r_free = 0.3765 target = 0.159473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124181 restraints weight = 3683.380| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.99 r_work: 0.3302 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3250 Z= 0.119 Angle : 0.512 7.279 4413 Z= 0.268 Chirality : 0.040 0.143 488 Planarity : 0.003 0.040 543 Dihedral : 4.808 47.340 480 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.00 % Allowed : 28.23 % Favored : 68.77 % 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: 1.31 (0.42), residues: 389 helix: 2.15 (0.35), residues: 214 sheet: 1.59 (0.96), residues: 27 loop : -1.28 (0.46), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 312 TYR 0.016 0.001 TYR A 132 PHE 0.018 0.001 PHE A 327 TRP 0.014 0.001 TRP A 23 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 3249) covalent geometry : angle 0.50958 / 0.27 ( 4411) SS BOND : bond 0.00927 / 0.49 ( 1) SS BOND : angle 2.24441 / 1.18 ( 2) hydrogen bonds : bond 0.04470 / 2.94 ( 174) hydrogen bonds : angle 3.96386 / 2.78 ( 510) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.074 Fit side-chains REVERT: A 1 MET cc_start: 0.4825 (OUTLIER) cc_final: 0.3801 (tpt) REVERT: A 20 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8653 (mp) REVERT: A 63 ASP cc_start: 0.7165 (p0) cc_final: 0.6608 (p0) REVERT: A 82 GLU cc_start: 0.8798 (pt0) cc_final: 0.8545 (pt0) REVERT: A 107 ASN cc_start: 0.8156 (m-40) cc_final: 0.7477 (t0) REVERT: A 138 ASP cc_start: 0.7634 (m-30) cc_final: 0.6894 (p0) REVERT: A 140 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8188 (mp) REVERT: A 161 MET cc_start: 0.8152 (tpp) cc_final: 0.7628 (mmt) REVERT: A 178 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: A 215 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8357 (mpt) REVERT: A 235 GLU cc_start: 0.7893 (pm20) cc_final: 0.7064 (pm20) REVERT: A 283 MET cc_start: 0.7604 (mtp) cc_final: 0.7319 (mmt) REVERT: A 373 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7755 (mp) outliers start: 10 outliers final: 4 residues processed: 61 average time/residue: 0.4186 time to fit residues: 26.4244 Evaluate side-chains 65 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 373 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: [33, 23, 19, 13, 9, 29, 22, 24, 31, 16, 17] chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 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 = 0.3747 r_free = 0.3747 target = 0.157823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.122431 restraints weight = 3638.553| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.99 r_work: 0.3254 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3250 Z= 0.134 Angle : 0.535 7.169 4413 Z= 0.280 Chirality : 0.041 0.139 488 Planarity : 0.004 0.040 543 Dihedral : 4.874 47.555 480 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.00 % Allowed : 28.83 % Favored : 68.17 % 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: 1.38 (0.42), residues: 389 helix: 2.22 (0.35), residues: 212 sheet: 1.59 (0.95), residues: 27 loop : -1.22 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 246 TYR 0.017 0.001 TYR A 132 PHE 0.018 0.001 PHE A 327 TRP 0.015 0.001 TRP A 23 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 3249) covalent geometry : angle 0.53333 / 0.28 ( 4411) SS BOND : bond 0.01015 / 0.53 ( 1) SS BOND : angle 2.30015 / 1.21 ( 2) hydrogen bonds : bond 0.04648 / 3.03 ( 174) hydrogen bonds : angle 3.98393 / 2.79 ( 510) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 778 Ramachandran restraints generated. 389 Oldfield, 0 Emsley, 389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.118 Fit side-chains REVERT: A 1 MET cc_start: 0.4889 (OUTLIER) cc_final: 0.3852 (tpt) REVERT: A 20 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8630 (mp) REVERT: A 63 ASP cc_start: 0.7157 (p0) cc_final: 0.6542 (p0) REVERT: A 82 GLU cc_start: 0.8749 (pt0) cc_final: 0.8481 (pt0) REVERT: A 107 ASN cc_start: 0.8200 (m-40) cc_final: 0.7521 (t0) REVERT: A 138 ASP cc_start: 0.7599 (m-30) cc_final: 0.6858 (p0) REVERT: A 140 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8125 (mp) REVERT: A 161 MET cc_start: 0.7986 (tpp) cc_final: 0.7635 (mmt) REVERT: A 178 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: A 215 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8303 (mpt) REVERT: A 235 GLU cc_start: 0.7859 (pm20) cc_final: 0.7007 (pm20) REVERT: A 283 MET cc_start: 0.7535 (mtp) cc_final: 0.7317 (mmt) REVERT: A 373 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7736 (mp) outliers start: 10 outliers final: 3 residues processed: 51 average time/residue: 0.4625 time to fit residues: 24.4026 Evaluate side-chains 54 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 373 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: [31, 8, 24, 37, 17, 29, 6, 15, 10, 27, 28] chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 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 = 0.3733 r_free = 0.3733 target = 0.156638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.121141 restraints weight = 3710.006| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.00 r_work: 0.3241 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3250 Z= 0.144 Angle : 0.544 6.898 4413 Z= 0.284 Chirality : 0.041 0.136 488 Planarity : 0.004 0.040 543 Dihedral : 4.920 47.220 480 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.70 % Allowed : 29.13 % Favored : 68.17 % 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: 1.13 (0.42), residues: 389 helix: 1.92 (0.34), residues: 218 sheet: 1.47 (0.94), residues: 27 loop : -1.30 (0.47), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 148 TYR 0.018 0.001 TYR A 132 PHE 0.018 0.002 PHE A 327 TRP 0.016 0.001 TRP A 23 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 3249) covalent geometry : angle 0.54160 / 0.28 ( 4411) SS BOND : bond 0.01081 / 0.57 ( 1) SS BOND : angle 2.37747 / 1.25 ( 2) hydrogen bonds : bond 0.04797 / 3.12 ( 174) hydrogen bonds : angle 4.01532 / 2.81 ( 510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1321.40 seconds wall clock time: 23 minutes 18.27 seconds (1398.27 seconds total)