Starting phenix.real_space_refine on Mon Jan 13 15:36:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ybe_39117/01_2025/8ybe_39117.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ybe_39117/01_2025/8ybe_39117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ybe_39117/01_2025/8ybe_39117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ybe_39117/01_2025/8ybe_39117.map" model { file = "/net/cci-nas-00/data/ceres_data/8ybe_39117/01_2025/8ybe_39117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ybe_39117/01_2025/8ybe_39117.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 6 5.16 5 C 1873 2.51 5 N 473 2.21 5 O 758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3110 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2890 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2879 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Conformer: "B" Number of residues, atoms: 370, 2879 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} bond proxies already assigned to first conformer: 2936 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Classifications: {'water': 197} Link IDs: {None: 196} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 393 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 393 " occ=0.50 Time building chain proxies: 4.00, per 1000 atoms: 1.29 Number of scatterers: 3110 At special positions: 0 Unit cell: (50.0692, 62.7628, 77.572, 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 6 16.00 O 758 8.00 N 473 7.00 C 1873 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 Links applied ALPHA1-4 " GLC B 1 " - " GLC B 2 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 682.1 milliseconds 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 684 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 4 sheets defined 54.9% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 42 through 58 Processing helix chain 'A' and resid 68 through 80 Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 90 through 100 removed outlier: 3.716A pdb=" N GLY A 94 " --> pdb=" O HIS A 90 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 115 Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 179 through 190 removed outlier: 3.768A pdb=" N THR A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 4.339A pdb=" N ASP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 227 Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.795A pdb=" N GLU A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 Processing helix chain 'A' and resid 360 through 379 removed outlier: 4.457A pdb=" N ALA A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 396 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 64 removed outlier: 6.350A pdb=" N LEU A 33 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLU A 64 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE A 35 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE A 85 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 34 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE A 87 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TRP A 36 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N ALA A 89 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA A 290 " --> pdb=" O PRO A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 8.222A pdb=" N SER A 171 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR A 251 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU A 173 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 10.897A pdb=" N ASN A 253 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA A 249 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 196 through 198 removed outlier: 3.668A pdb=" N LYS A 196 " --> pdb=" O ASP A 203 " (cutoff:3.500A) 149 hydrogen bonds defined for protein. 433 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: 0.88 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 544 1.32 - 1.44: 729 1.44 - 1.56: 1698 1.56 - 1.68: 0 1.68 - 1.81: 12 Bond restraints: 2983 Sorted by residual: bond pdb=" C ALA A 172 " pdb=" O ALA A 172 " ideal model delta sigma weight residual 1.236 1.199 0.037 1.15e-02 7.56e+03 1.05e+01 bond pdb=" CA ARG A 380 " pdb=" C ARG A 380 " ideal model delta sigma weight residual 1.524 1.484 0.039 1.29e-02 6.01e+03 9.19e+00 bond pdb=" CA LYS A 201 " pdb=" C LYS A 201 " ideal model delta sigma weight residual 1.519 1.486 0.034 1.14e-02 7.69e+03 8.68e+00 bond pdb=" C ALA A 327 " pdb=" O ALA A 327 " ideal model delta sigma weight residual 1.234 1.202 0.032 1.22e-02 6.72e+03 6.97e+00 bond pdb=" CA LYS A 32 " pdb=" C LYS A 32 " ideal model delta sigma weight residual 1.521 1.489 0.032 1.24e-02 6.50e+03 6.66e+00 ... (remaining 2978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 3842 1.80 - 3.60: 166 3.60 - 5.40: 33 5.40 - 7.20: 6 7.20 - 9.00: 3 Bond angle restraints: 4050 Sorted by residual: angle pdb=" N PRO A 357 " pdb=" CA PRO A 357 " pdb=" C PRO A 357 " ideal model delta sigma weight residual 111.68 102.68 9.00 1.67e+00 3.59e-01 2.90e+01 angle pdb=" N SER A 296 " pdb=" CA SER A 296 " pdb=" C SER A 296 " ideal model delta sigma weight residual 109.48 116.86 -7.38 1.44e+00 4.82e-01 2.63e+01 angle pdb=" N PRO A 297 " pdb=" CA PRO A 297 " pdb=" C PRO A 297 " ideal model delta sigma weight residual 114.35 108.38 5.97 1.25e+00 6.40e-01 2.28e+01 angle pdb=" C MET A 356 " pdb=" N PRO A 357 " pdb=" CA PRO A 357 " ideal model delta sigma weight residual 120.14 115.17 4.97 1.06e+00 8.90e-01 2.20e+01 angle pdb=" O ASP A 91 " pdb=" C ASP A 91 " pdb=" N ARG A 92 " ideal model delta sigma weight residual 122.20 127.09 -4.89 1.14e+00 7.69e-01 1.84e+01 ... (remaining 4045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 1614 17.04 - 34.09: 132 34.09 - 51.13: 48 51.13 - 68.17: 16 68.17 - 85.21: 4 Dihedral angle restraints: 1814 sinusoidal: 744 harmonic: 1070 Sorted by residual: dihedral pdb=" CA ASP A 56 " pdb=" C ASP A 56 " pdb=" N THR A 57 " pdb=" CA THR A 57 " ideal model delta harmonic sigma weight residual 180.00 -164.28 -15.72 0 5.00e+00 4.00e-02 9.89e+00 dihedral pdb=" CB GLU A 137 " pdb=" CG GLU A 137 " pdb=" CD GLU A 137 " pdb=" OE1 GLU A 137 " ideal model delta sinusoidal sigma weight residual 0.00 85.21 -85.21 1 3.00e+01 1.11e-03 9.78e+00 dihedral pdb=" N GLN A 381 " pdb=" CA GLN A 381 " pdb=" CB GLN A 381 " pdb=" CG GLN A 381 " ideal model delta sinusoidal sigma weight residual -180.00 -121.35 -58.65 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 1811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 374 0.068 - 0.136: 65 0.136 - 0.204: 6 0.204 - 0.273: 0 0.273 - 0.341: 1 Chirality restraints: 446 Sorted by residual: chirality pdb=" C1 GLC B 2 " pdb=" O4 GLC B 1 " pdb=" C2 GLC B 2 " pdb=" O5 GLC B 2 " both_signs ideal model delta sigma weight residual False 2.40 2.44 -0.04 2.00e-02 2.50e+03 4.34e+00 chirality pdb=" C1 GLC B 1 " pdb=" C2 GLC B 1 " pdb=" O1 GLC B 1 " pdb=" O5 GLC B 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.38 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA MET A 347 " pdb=" N MET A 347 " pdb=" C MET A 347 " pdb=" CB MET A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 443 not shown) Planarity restraints: 521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 92 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.97e+01 pdb=" C ARG A 92 " 0.077 2.00e-02 2.50e+03 pdb=" O ARG A 92 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE A 93 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 392 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C THR A 392 " 0.049 2.00e-02 2.50e+03 pdb=" O THR A 392 " -0.018 2.00e-02 2.50e+03 pdb=" N AARG A 393 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 392 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C THR A 392 " 0.048 2.00e-02 2.50e+03 pdb=" O THR A 392 " -0.018 2.00e-02 2.50e+03 pdb=" N BARG A 393 " -0.016 2.00e-02 2.50e+03 ... (remaining 518 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 772 2.77 - 3.30: 3381 3.30 - 3.83: 6978 3.83 - 4.37: 8256 4.37 - 4.90: 12524 Nonbonded interactions: 31911 Sorted by model distance: nonbonded pdb=" OH TYR A 193 " pdb=" OD1 ASP A 206 " model vdw 2.236 3.040 nonbonded pdb=" O VAL A 76 " pdb=" OG1 THR A 79 " model vdw 2.298 3.040 nonbonded pdb=" O HOH A 454 " pdb=" O HOH A 592 " model vdw 2.327 3.040 nonbonded pdb=" OD2 ASP A 262 " pdb=" O HOH A 401 " model vdw 2.330 3.040 nonbonded pdb=" O THR A 248 " pdb=" O HOH A 402 " model vdw 2.330 3.040 ... (remaining 31906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.50 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: 1.150 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.960 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.006 0.042 2983 Z= 0.400 Angle : 0.888 9.000 4050 Z= 0.529 Chirality : 0.053 0.341 446 Planarity : 0.008 0.061 521 Dihedral : 15.835 85.214 1130 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.34 % Allowed : 13.38 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.41), residues: 371 helix: 0.91 (0.33), residues: 192 sheet: 0.98 (0.79), residues: 29 loop : 1.15 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 88 HIS 0.004 0.001 HIS A 229 PHE 0.013 0.002 PHE A 220 TYR 0.022 0.002 TYR A 181 ARG 0.003 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.355 Fit side-chains REVERT: A 29 GLU cc_start: 0.6751 (tt0) cc_final: 0.5984 (mm-30) REVERT: A 98 GLN cc_start: 0.7692 (tp40) cc_final: 0.7436 (tm-30) REVERT: A 128 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7932 (mtpm) REVERT: A 197 TYR cc_start: 0.7370 (t80) cc_final: 0.6600 (t80) REVERT: A 284 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.6140 (m-10) REVERT: A 354 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6670 (pm20) outliers start: 6 outliers final: 1 residues processed: 55 average time/residue: 1.3972 time to fit residues: 78.9033 Evaluate side-chains 37 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 284 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.144435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128530 restraints weight = 11280.863| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.83 r_work: 0.3274 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2983 Z= 0.249 Angle : 0.640 7.031 4050 Z= 0.340 Chirality : 0.044 0.153 446 Planarity : 0.005 0.054 521 Dihedral : 6.920 64.579 439 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.34 % Allowed : 15.72 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.42), residues: 371 helix: 0.89 (0.34), residues: 192 sheet: 0.66 (0.98), residues: 24 loop : 1.43 (0.53), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 184 HIS 0.002 0.001 HIS A 90 PHE 0.012 0.002 PHE A 220 TYR 0.024 0.002 TYR A 181 ARG 0.001 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.299 Fit side-chains REVERT: A 98 GLN cc_start: 0.7926 (tp40) cc_final: 0.7617 (tm-30) REVERT: A 128 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7857 (mtpm) REVERT: A 179 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8178 (mm-30) outliers start: 6 outliers final: 1 residues processed: 46 average time/residue: 1.3812 time to fit residues: 65.3733 Evaluate side-chains 38 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 0.0980 chunk 33 optimal weight: 0.4980 chunk 6 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.146744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131626 restraints weight = 10929.584| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.70 r_work: 0.3312 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2983 Z= 0.216 Angle : 0.586 6.881 4050 Z= 0.307 Chirality : 0.042 0.121 446 Planarity : 0.005 0.050 521 Dihedral : 5.167 53.201 436 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.00 % Allowed : 16.39 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.44), residues: 371 helix: 0.90 (0.35), residues: 192 sheet: 0.31 (0.96), residues: 24 loop : 1.52 (0.56), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 184 HIS 0.003 0.002 HIS A 90 PHE 0.011 0.002 PHE A 175 TYR 0.020 0.001 TYR A 181 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.328 Fit side-chains REVERT: A 98 GLN cc_start: 0.7966 (tp40) cc_final: 0.7712 (tm-30) REVERT: A 321 LYS cc_start: 0.8132 (mptp) cc_final: 0.7611 (tttm) outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 1.4063 time to fit residues: 66.5121 Evaluate side-chains 36 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.145591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.132594 restraints weight = 5871.099| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.27 r_work: 0.3369 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2983 Z= 0.231 Angle : 0.595 6.824 4050 Z= 0.309 Chirality : 0.042 0.119 446 Planarity : 0.005 0.049 521 Dihedral : 5.190 53.080 436 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.00 % Allowed : 16.72 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.44), residues: 371 helix: 0.90 (0.35), residues: 192 sheet: 0.03 (0.96), residues: 24 loop : 1.55 (0.56), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 184 HIS 0.004 0.002 HIS A 90 PHE 0.012 0.002 PHE A 243 TYR 0.016 0.001 TYR A 181 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.353 Fit side-chains REVERT: A 92 ARG cc_start: 0.8159 (mmt180) cc_final: 0.7639 (mmm160) REVERT: A 98 GLN cc_start: 0.7881 (tp40) cc_final: 0.7620 (tm-30) REVERT: A 203 ASP cc_start: 0.7788 (t0) cc_final: 0.7448 (t0) REVERT: A 321 LYS cc_start: 0.7921 (mptp) cc_final: 0.7382 (tttm) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 1.5144 time to fit residues: 66.8499 Evaluate side-chains 38 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.141573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126713 restraints weight = 8323.167| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.56 r_work: 0.3268 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2983 Z= 0.283 Angle : 0.640 7.196 4050 Z= 0.332 Chirality : 0.044 0.120 446 Planarity : 0.005 0.049 521 Dihedral : 5.321 52.353 436 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.00 % Allowed : 16.72 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.44), residues: 371 helix: 0.85 (0.35), residues: 192 sheet: -0.18 (0.98), residues: 24 loop : 1.61 (0.57), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 184 HIS 0.005 0.002 HIS A 90 PHE 0.014 0.003 PHE A 243 TYR 0.015 0.002 TYR A 181 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.345 Fit side-chains REVERT: A 27 LYS cc_start: 0.5395 (OUTLIER) cc_final: 0.4788 (mtmt) REVERT: A 98 GLN cc_start: 0.7931 (tp40) cc_final: 0.7636 (tm-30) REVERT: A 203 ASP cc_start: 0.7818 (t0) cc_final: 0.7401 (t0) REVERT: A 284 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.6036 (m-10) REVERT: A 304 GLU cc_start: 0.8424 (tp30) cc_final: 0.8176 (tp30) REVERT: A 321 LYS cc_start: 0.7994 (mptp) cc_final: 0.7417 (tttm) outliers start: 2 outliers final: 0 residues processed: 42 average time/residue: 1.3682 time to fit residues: 59.1057 Evaluate side-chains 37 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 284 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.144277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128587 restraints weight = 9669.255| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.73 r_work: 0.3295 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2983 Z= 0.235 Angle : 0.599 6.745 4050 Z= 0.309 Chirality : 0.042 0.119 446 Planarity : 0.004 0.047 521 Dihedral : 5.218 53.149 436 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.34 % Allowed : 16.39 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.45), residues: 371 helix: 0.86 (0.35), residues: 192 sheet: -0.32 (0.99), residues: 24 loop : 1.61 (0.57), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 184 HIS 0.004 0.002 HIS A 90 PHE 0.012 0.002 PHE A 243 TYR 0.015 0.001 TYR A 181 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.346 Fit side-chains REVERT: A 27 LYS cc_start: 0.5415 (OUTLIER) cc_final: 0.4841 (mtmt) REVERT: A 92 ARG cc_start: 0.8218 (mmt180) cc_final: 0.7760 (mmm160) REVERT: A 98 GLN cc_start: 0.7923 (tp40) cc_final: 0.7670 (tm-30) REVERT: A 304 GLU cc_start: 0.8434 (tp30) cc_final: 0.8161 (tp30) REVERT: A 321 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7410 (tttm) outliers start: 3 outliers final: 1 residues processed: 41 average time/residue: 1.4876 time to fit residues: 62.5476 Evaluate side-chains 39 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 321 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.130419 restraints weight = 5902.636| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.28 r_work: 0.3342 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2983 Z= 0.250 Angle : 0.610 6.908 4050 Z= 0.315 Chirality : 0.042 0.119 446 Planarity : 0.005 0.047 521 Dihedral : 5.264 53.106 436 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.34 % Allowed : 16.39 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.45), residues: 371 helix: 0.77 (0.35), residues: 195 sheet: -0.40 (1.00), residues: 24 loop : 1.63 (0.59), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 184 HIS 0.005 0.002 HIS A 90 PHE 0.013 0.002 PHE A 243 TYR 0.015 0.001 TYR A 181 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.355 Fit side-chains REVERT: A 27 LYS cc_start: 0.5476 (OUTLIER) cc_final: 0.5274 (pttp) REVERT: A 92 ARG cc_start: 0.8204 (mmt180) cc_final: 0.7755 (mmm160) REVERT: A 98 GLN cc_start: 0.7871 (tp40) cc_final: 0.7657 (tm-30) REVERT: A 237 SER cc_start: 0.8360 (m) cc_final: 0.8133 (t) REVERT: A 304 GLU cc_start: 0.8345 (tp30) cc_final: 0.8070 (tp30) REVERT: A 321 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7385 (tttm) outliers start: 3 outliers final: 1 residues processed: 41 average time/residue: 1.4272 time to fit residues: 60.1522 Evaluate side-chains 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 321 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 5 optimal weight: 0.0470 chunk 25 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.147901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131714 restraints weight = 10355.807| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.83 r_work: 0.3320 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2983 Z= 0.199 Angle : 0.575 6.419 4050 Z= 0.295 Chirality : 0.041 0.118 446 Planarity : 0.004 0.046 521 Dihedral : 5.107 53.510 436 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.00 % Allowed : 17.73 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.45), residues: 371 helix: 0.86 (0.36), residues: 195 sheet: -0.41 (1.01), residues: 24 loop : 1.59 (0.58), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 184 HIS 0.004 0.002 HIS A 90 PHE 0.011 0.002 PHE A 243 TYR 0.015 0.001 TYR A 181 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.338 Fit side-chains REVERT: A 92 ARG cc_start: 0.8175 (mmt180) cc_final: 0.7730 (mmm160) REVERT: A 98 GLN cc_start: 0.7904 (tp40) cc_final: 0.7649 (tm-30) REVERT: A 304 GLU cc_start: 0.8418 (tp30) cc_final: 0.8162 (tp30) REVERT: A 314 GLU cc_start: 0.7278 (mp0) cc_final: 0.7023 (mp0) REVERT: A 321 LYS cc_start: 0.7948 (mptp) cc_final: 0.7366 (tttm) outliers start: 2 outliers final: 1 residues processed: 42 average time/residue: 1.5185 time to fit residues: 65.5361 Evaluate side-chains 36 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 0.0020 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.147040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.132266 restraints weight = 7601.297| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.53 r_work: 0.3347 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2983 Z= 0.218 Angle : 0.592 6.592 4050 Z= 0.303 Chirality : 0.042 0.121 446 Planarity : 0.004 0.046 521 Dihedral : 5.131 53.288 436 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.67 % Allowed : 17.73 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.45), residues: 371 helix: 0.84 (0.36), residues: 195 sheet: -0.40 (1.01), residues: 24 loop : 1.55 (0.58), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 184 HIS 0.004 0.002 HIS A 90 PHE 0.012 0.002 PHE A 243 TYR 0.015 0.001 TYR A 181 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.319 Fit side-chains REVERT: A 92 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7732 (mmm160) REVERT: A 98 GLN cc_start: 0.7892 (tp40) cc_final: 0.7657 (tm-30) REVERT: A 304 GLU cc_start: 0.8387 (tp30) cc_final: 0.8124 (tp30) REVERT: A 314 GLU cc_start: 0.7224 (mp0) cc_final: 0.6941 (mp0) REVERT: A 321 LYS cc_start: 0.7919 (mptp) cc_final: 0.7370 (tttm) outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 1.4805 time to fit residues: 59.3483 Evaluate side-chains 38 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.0670 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 8 optimal weight: 2.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.147510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132513 restraints weight = 7987.554| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.58 r_work: 0.3347 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2983 Z= 0.214 Angle : 0.590 6.693 4050 Z= 0.301 Chirality : 0.041 0.119 446 Planarity : 0.004 0.046 521 Dihedral : 5.116 53.474 436 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.00 % Allowed : 17.06 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.45), residues: 371 helix: 0.84 (0.36), residues: 195 sheet: -0.40 (1.00), residues: 24 loop : 1.58 (0.58), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 184 HIS 0.004 0.002 HIS A 90 PHE 0.011 0.002 PHE A 243 TYR 0.014 0.001 TYR A 181 ARG 0.001 0.000 ARG A 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.319 Fit side-chains REVERT: A 92 ARG cc_start: 0.8123 (mmt180) cc_final: 0.7732 (mmm160) REVERT: A 98 GLN cc_start: 0.7903 (tp40) cc_final: 0.7664 (tm-30) REVERT: A 304 GLU cc_start: 0.8381 (tp30) cc_final: 0.8129 (tp30) REVERT: A 314 GLU cc_start: 0.7224 (mp0) cc_final: 0.6961 (mp0) REVERT: A 321 LYS cc_start: 0.7944 (mptp) cc_final: 0.7379 (tttm) outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 1.4440 time to fit residues: 59.4382 Evaluate side-chains 37 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.140763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128738 restraints weight = 4588.609| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.09 r_work: 0.3332 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 2983 Z= 0.321 Angle : 0.675 7.578 4050 Z= 0.347 Chirality : 0.044 0.123 446 Planarity : 0.005 0.048 521 Dihedral : 5.341 52.139 436 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.00 % Allowed : 18.39 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.44), residues: 371 helix: 0.78 (0.35), residues: 192 sheet: -0.55 (1.01), residues: 24 loop : 1.56 (0.57), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 184 HIS 0.007 0.002 HIS A 90 PHE 0.015 0.003 PHE A 243 TYR 0.014 0.002 TYR A 181 ARG 0.002 0.001 ARG A 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3025.89 seconds wall clock time: 54 minutes 14.49 seconds (3254.49 seconds total)