Starting phenix.real_space_refine on Tue Feb 11 02:43:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zj2_14739/02_2025/7zj2_14739.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zj2_14739/02_2025/7zj2_14739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zj2_14739/02_2025/7zj2_14739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zj2_14739/02_2025/7zj2_14739.map" model { file = "/net/cci-nas-00/data/ceres_data/7zj2_14739/02_2025/7zj2_14739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zj2_14739/02_2025/7zj2_14739.cif" } resolution = 3.32 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= 0.032 sd= 0.409 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 12 5.16 5 C 2292 2.51 5 N 696 2.21 5 O 792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3792 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 1.61, per 1000 atoms: 0.42 Number of scatterers: 3792 At special positions: 0 Unit cell: (73.84, 75.92, 47.84, 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 12 16.00 O 792 8.00 N 696 7.00 C 2292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 465.9 milliseconds 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 696 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 272 removed outlier: 6.560A pdb=" N GLN A 269 " --> pdb=" O SER C 270 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ASN C 272 " --> pdb=" O GLN A 269 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER A 271 " --> pdb=" O ASN C 272 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN C 269 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN E 272 " --> pdb=" O GLN C 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER C 271 " --> pdb=" O ASN E 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN E 269 " --> pdb=" O SER G 270 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ASN G 272 " --> pdb=" O GLN E 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER E 271 " --> pdb=" O ASN G 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN G 269 " --> pdb=" O SER I 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN I 272 " --> pdb=" O GLN G 269 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER G 271 " --> pdb=" O ASN I 272 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN I 269 " --> pdb=" O SER K 270 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ASN K 272 " --> pdb=" O GLN I 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER I 271 " --> pdb=" O ASN K 272 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 272 removed outlier: 6.560A pdb=" N GLN B 269 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN D 272 " --> pdb=" O GLN B 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER B 271 " --> pdb=" O ASN D 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN D 269 " --> pdb=" O SER F 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN F 272 " --> pdb=" O GLN D 269 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER D 271 " --> pdb=" O ASN F 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN F 269 " --> pdb=" O SER H 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN H 272 " --> pdb=" O GLN F 269 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER F 271 " --> pdb=" O ASN H 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN H 269 " --> pdb=" O SER J 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN J 272 " --> pdb=" O GLN H 269 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER H 271 " --> pdb=" O ASN J 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN J 269 " --> pdb=" O SER L 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN L 272 " --> pdb=" O GLN J 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER J 271 " --> pdb=" O ASN L 272 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 No hydrogen bonds 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: 0.05 Time building geometry restraints manager: 0.90 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: 672 1.31 - 1.43: 1368 1.43 - 1.56: 1836 1.56 - 1.68: 0 1.68 - 1.81: 24 Bond restraints: 3900 Sorted by residual: bond pdb=" C PRO L 288 " pdb=" O PRO L 288 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.16e-02 7.43e+03 1.99e+01 bond pdb=" C PRO I 288 " pdb=" O PRO I 288 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.16e-02 7.43e+03 1.99e+01 bond pdb=" C PRO A 288 " pdb=" O PRO A 288 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.16e-02 7.43e+03 1.99e+01 bond pdb=" C PRO E 288 " pdb=" O PRO E 288 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.16e-02 7.43e+03 1.98e+01 bond pdb=" C PRO F 288 " pdb=" O PRO F 288 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.16e-02 7.43e+03 1.98e+01 ... (remaining 3895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 3217 1.63 - 3.25: 1000 3.25 - 4.88: 806 4.88 - 6.50: 149 6.50 - 8.13: 12 Bond angle restraints: 5184 Sorted by residual: angle pdb=" CA GLY A 291 " pdb=" C GLY A 291 " pdb=" O GLY A 291 " ideal model delta sigma weight residual 122.23 117.52 4.71 6.90e-01 2.10e+00 4.67e+01 angle pdb=" CA GLY I 291 " pdb=" C GLY I 291 " pdb=" O GLY I 291 " ideal model delta sigma weight residual 122.23 117.54 4.69 6.90e-01 2.10e+00 4.62e+01 angle pdb=" CA GLY C 291 " pdb=" C GLY C 291 " pdb=" O GLY C 291 " ideal model delta sigma weight residual 122.23 117.55 4.68 6.90e-01 2.10e+00 4.60e+01 angle pdb=" CA GLY G 291 " pdb=" C GLY G 291 " pdb=" O GLY G 291 " ideal model delta sigma weight residual 122.23 117.56 4.67 6.90e-01 2.10e+00 4.58e+01 angle pdb=" CA GLY K 291 " pdb=" C GLY K 291 " pdb=" O GLY K 291 " ideal model delta sigma weight residual 122.23 117.56 4.67 6.90e-01 2.10e+00 4.58e+01 ... (remaining 5179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 1779 14.96 - 29.91: 177 29.91 - 44.86: 12 44.86 - 59.82: 24 59.82 - 74.77: 24 Dihedral angle restraints: 2016 sinusoidal: 744 harmonic: 1272 Sorted by residual: dihedral pdb=" CA ASN J 268 " pdb=" CB ASN J 268 " pdb=" CG ASN J 268 " pdb=" OD1 ASN J 268 " ideal model delta sinusoidal sigma weight residual -90.00 -160.75 70.75 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASN F 268 " pdb=" CB ASN F 268 " pdb=" CG ASN F 268 " pdb=" OD1 ASN F 268 " ideal model delta sinusoidal sigma weight residual -90.00 -160.74 70.74 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASN L 268 " pdb=" CB ASN L 268 " pdb=" CG ASN L 268 " pdb=" OD1 ASN L 268 " ideal model delta sinusoidal sigma weight residual -90.00 -160.74 70.74 2 2.00e+01 2.50e-03 1.07e+01 ... (remaining 2013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 120 0.034 - 0.068: 96 0.068 - 0.102: 48 0.102 - 0.136: 36 0.136 - 0.170: 48 Chirality restraints: 348 Sorted by residual: chirality pdb=" CA TYR F 260 " pdb=" N TYR F 260 " pdb=" C TYR F 260 " pdb=" CB TYR F 260 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA TYR J 260 " pdb=" N TYR J 260 " pdb=" C TYR J 260 " pdb=" CB TYR J 260 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA TYR H 260 " pdb=" N TYR H 260 " pdb=" C TYR H 260 " pdb=" CB TYR H 260 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 345 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 270 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C SER J 270 " -0.058 2.00e-02 2.50e+03 pdb=" O SER J 270 " 0.022 2.00e-02 2.50e+03 pdb=" N SER J 271 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 270 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C SER E 270 " 0.058 2.00e-02 2.50e+03 pdb=" O SER E 270 " -0.022 2.00e-02 2.50e+03 pdb=" N SER E 271 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 270 " 0.016 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C SER L 270 " -0.058 2.00e-02 2.50e+03 pdb=" O SER L 270 " 0.022 2.00e-02 2.50e+03 pdb=" N SER L 271 " 0.020 2.00e-02 2.50e+03 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 2390 3.02 - 3.49: 3846 3.49 - 3.96: 6869 3.96 - 4.43: 7785 4.43 - 4.90: 15100 Nonbonded interactions: 35990 Sorted by model distance: nonbonded pdb=" N SER F 286 " pdb=" O SER F 286 " model vdw 2.548 2.496 nonbonded pdb=" N SER L 286 " pdb=" O SER L 286 " model vdw 2.548 2.496 nonbonded pdb=" N SER D 286 " pdb=" O SER D 286 " model vdw 2.548 2.496 nonbonded pdb=" N SER B 286 " pdb=" O SER B 286 " model vdw 2.548 2.496 nonbonded pdb=" N SER H 286 " pdb=" O SER H 286 " model vdw 2.548 2.496 ... (remaining 35985 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.900 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.014 0.054 3900 Z= 1.050 Angle : 2.210 8.127 5184 Z= 1.661 Chirality : 0.082 0.170 348 Planarity : 0.011 0.034 780 Dihedral : 15.288 74.770 1320 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 24.14 % Favored : 75.86 % 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: -3.75 (0.24), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.18), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.004 PHE F 273 TYR 0.029 0.004 TYR D 260 ARG 0.003 0.001 ARG F 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 263 PHE cc_start: 0.8219 (p90) cc_final: 0.7186 (m-80) REVERT: A 284 ARG cc_start: 0.8298 (ttt180) cc_final: 0.6213 (mtm-85) REVERT: A 289 TYR cc_start: 0.8718 (m-80) cc_final: 0.6974 (p90) REVERT: B 263 PHE cc_start: 0.8106 (p90) cc_final: 0.7124 (m-80) REVERT: B 266 TYR cc_start: 0.8254 (m-80) cc_final: 0.7926 (m-80) REVERT: B 284 ARG cc_start: 0.8026 (ttt180) cc_final: 0.5448 (mpt180) REVERT: B 289 TYR cc_start: 0.8639 (m-80) cc_final: 0.6974 (p90) REVERT: C 252 SER cc_start: 0.8580 (m) cc_final: 0.8242 (m) REVERT: C 266 TYR cc_start: 0.8270 (m-80) cc_final: 0.8007 (m-80) REVERT: G 266 TYR cc_start: 0.8346 (m-80) cc_final: 0.8126 (m-80) REVERT: H 266 TYR cc_start: 0.8347 (m-80) cc_final: 0.8105 (m-80) REVERT: J 263 PHE cc_start: 0.8410 (p90) cc_final: 0.8188 (p90) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1620 time to fit residues: 47.1500 Evaluate side-chains 180 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.144673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.133403 restraints weight = 6647.836| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.96 r_work: 0.4145 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3900 Z= 0.145 Angle : 0.569 4.564 5184 Z= 0.331 Chirality : 0.030 0.075 348 Planarity : 0.004 0.022 780 Dihedral : 4.426 10.541 588 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.46 % Allowed : 23.85 % Favored : 70.69 % 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: -3.65 (0.25), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.19), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.002 PHE C 263 TYR 0.023 0.002 TYR I 260 ARG 0.004 0.001 ARG F 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.386 Fit side-chains REVERT: A 263 PHE cc_start: 0.8737 (p90) cc_final: 0.6898 (m-10) REVERT: A 284 ARG cc_start: 0.8680 (ttt180) cc_final: 0.5410 (mtt90) REVERT: A 289 TYR cc_start: 0.9059 (m-80) cc_final: 0.7003 (p90) REVERT: B 263 PHE cc_start: 0.8855 (p90) cc_final: 0.6708 (m-80) REVERT: B 266 TYR cc_start: 0.8707 (m-80) cc_final: 0.7992 (m-80) REVERT: B 289 TYR cc_start: 0.8885 (m-80) cc_final: 0.6895 (p90) REVERT: C 252 SER cc_start: 0.8382 (m) cc_final: 0.8063 (m) REVERT: C 260 TYR cc_start: 0.8277 (t80) cc_final: 0.8072 (t80) REVERT: C 263 PHE cc_start: 0.9123 (p90) cc_final: 0.8695 (p90) REVERT: D 276 MET cc_start: 0.9458 (ttp) cc_final: 0.9235 (tmm) REVERT: E 266 TYR cc_start: 0.9334 (m-80) cc_final: 0.8745 (m-80) REVERT: F 276 MET cc_start: 0.9264 (ttp) cc_final: 0.8971 (ttp) REVERT: H 276 MET cc_start: 0.9012 (ttp) cc_final: 0.8808 (tmm) REVERT: I 263 PHE cc_start: 0.9106 (p90) cc_final: 0.8604 (p90) REVERT: I 276 MET cc_start: 0.9009 (ttp) cc_final: 0.7980 (ttp) REVERT: J 252 SER cc_start: 0.8316 (m) cc_final: 0.7776 (m) REVERT: J 263 PHE cc_start: 0.9184 (p90) cc_final: 0.8924 (p90) REVERT: J 266 TYR cc_start: 0.9269 (m-80) cc_final: 0.8931 (m-80) REVERT: J 276 MET cc_start: 0.9023 (ttp) cc_final: 0.7993 (ttp) REVERT: K 260 TYR cc_start: 0.8478 (t80) cc_final: 0.8255 (t80) REVERT: K 276 MET cc_start: 0.9148 (ttt) cc_final: 0.8814 (ttp) REVERT: K 280 ASN cc_start: 0.7855 (p0) cc_final: 0.7084 (t0) REVERT: L 266 TYR cc_start: 0.9058 (m-80) cc_final: 0.8766 (m-80) REVERT: L 280 ASN cc_start: 0.8193 (p0) cc_final: 0.6709 (m-40) REVERT: L 281 PHE cc_start: 0.7465 (m-80) cc_final: 0.6954 (m-80) REVERT: L 289 TYR cc_start: 0.8636 (m-80) cc_final: 0.8434 (m-80) outliers start: 19 outliers final: 14 residues processed: 167 average time/residue: 0.1294 time to fit residues: 27.3454 Evaluate side-chains 159 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain L residue 252 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN I 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.133405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.123179 restraints weight = 6901.126| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.77 r_work: 0.3978 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.037 3900 Z= 0.364 Angle : 0.600 4.265 5184 Z= 0.346 Chirality : 0.032 0.092 348 Planarity : 0.004 0.024 780 Dihedral : 5.209 11.841 588 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.62 % Allowed : 23.56 % Favored : 67.82 % 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: -3.70 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.039 0.004 PHE L 263 TYR 0.018 0.002 TYR A 260 ARG 0.003 0.001 ARG J 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.436 Fit side-chains REVERT: A 295 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: B 281 PHE cc_start: 0.7335 (m-80) cc_final: 0.7126 (m-80) REVERT: C 261 ASN cc_start: 0.9408 (m-40) cc_final: 0.9022 (m-40) REVERT: C 266 TYR cc_start: 0.9229 (m-80) cc_final: 0.9004 (m-80) REVERT: D 276 MET cc_start: 0.9520 (ttp) cc_final: 0.8968 (tmm) REVERT: F 259 SER cc_start: 0.9004 (OUTLIER) cc_final: 0.8525 (p) REVERT: F 295 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: G 276 MET cc_start: 0.9506 (ttp) cc_final: 0.8594 (tmm) REVERT: H 276 MET cc_start: 0.9149 (ttp) cc_final: 0.8783 (ttp) REVERT: I 276 MET cc_start: 0.9204 (ttp) cc_final: 0.8782 (ttp) REVERT: J 252 SER cc_start: 0.8546 (m) cc_final: 0.8201 (p) REVERT: J 261 ASN cc_start: 0.9382 (m-40) cc_final: 0.9028 (m-40) REVERT: J 266 TYR cc_start: 0.9309 (m-80) cc_final: 0.8929 (m-80) REVERT: K 262 ASP cc_start: 0.8469 (t0) cc_final: 0.8260 (t0) REVERT: K 272 ASN cc_start: 0.6387 (t0) cc_final: 0.6054 (p0) REVERT: L 272 ASN cc_start: 0.6853 (t0) cc_final: 0.6482 (p0) outliers start: 30 outliers final: 23 residues processed: 144 average time/residue: 0.1246 time to fit residues: 22.8608 Evaluate side-chains 152 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 270 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 270 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 265 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 = 0.4234 r_free = 0.4234 target = 0.133632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.123008 restraints weight = 6980.876| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.74 r_work: 0.4051 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3900 Z= 0.214 Angle : 0.522 3.711 5184 Z= 0.296 Chirality : 0.030 0.085 348 Planarity : 0.003 0.020 780 Dihedral : 4.422 11.964 588 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 9.20 % Allowed : 23.85 % Favored : 66.95 % 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: -3.72 (0.21), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.16), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.029 0.003 PHE E 281 TYR 0.020 0.002 TYR D 266 ARG 0.004 0.001 ARG J 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.425 Fit side-chains REVERT: A 289 TYR cc_start: 0.8989 (m-80) cc_final: 0.6850 (p90) REVERT: A 295 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7620 (m-80) REVERT: B 266 TYR cc_start: 0.8841 (m-80) cc_final: 0.8513 (m-80) REVERT: B 289 TYR cc_start: 0.8850 (m-80) cc_final: 0.6876 (p90) REVERT: C 261 ASN cc_start: 0.9336 (m-40) cc_final: 0.9088 (m-40) REVERT: C 266 TYR cc_start: 0.9177 (m-80) cc_final: 0.8925 (m-80) REVERT: C 295 TYR cc_start: 0.7722 (OUTLIER) cc_final: 0.7343 (m-80) REVERT: D 263 PHE cc_start: 0.9201 (p90) cc_final: 0.8805 (p90) REVERT: D 276 MET cc_start: 0.9510 (ttp) cc_final: 0.9175 (tmm) REVERT: F 276 MET cc_start: 0.9278 (ttp) cc_final: 0.8730 (tmm) REVERT: F 295 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.7056 (m-80) REVERT: H 266 TYR cc_start: 0.9387 (m-80) cc_final: 0.9113 (m-80) REVERT: I 276 MET cc_start: 0.9213 (ttp) cc_final: 0.8994 (ttp) REVERT: J 252 SER cc_start: 0.8477 (m) cc_final: 0.8137 (p) REVERT: J 261 ASN cc_start: 0.9304 (m-40) cc_final: 0.8883 (m-40) REVERT: J 266 TYR cc_start: 0.9316 (m-80) cc_final: 0.8754 (m-80) REVERT: K 272 ASN cc_start: 0.6416 (t0) cc_final: 0.6189 (p0) REVERT: L 272 ASN cc_start: 0.6718 (t0) cc_final: 0.6418 (p0) REVERT: L 276 MET cc_start: 0.8156 (ttp) cc_final: 0.6876 (tpt) REVERT: L 280 ASN cc_start: 0.7455 (p0) cc_final: 0.6358 (t0) REVERT: L 295 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.7182 (m-80) outliers start: 32 outliers final: 23 residues processed: 150 average time/residue: 0.1210 time to fit residues: 23.2218 Evaluate side-chains 159 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 295 TYR Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 295 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 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 = 0.4238 r_free = 0.4238 target = 0.133814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.123027 restraints weight = 7080.175| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.83 r_work: 0.3971 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.031 3900 Z= 0.345 Angle : 0.573 4.387 5184 Z= 0.327 Chirality : 0.031 0.085 348 Planarity : 0.003 0.018 780 Dihedral : 4.826 13.749 588 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 10.34 % Allowed : 24.43 % Favored : 65.23 % 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: -3.77 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.032 0.004 PHE E 281 TYR 0.020 0.002 TYR D 266 ARG 0.003 0.001 ARG J 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.420 Fit side-chains REVERT: A 295 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: B 281 PHE cc_start: 0.7612 (m-80) cc_final: 0.7328 (m-80) REVERT: C 261 ASN cc_start: 0.9373 (m-40) cc_final: 0.9108 (m-40) REVERT: C 266 TYR cc_start: 0.9337 (m-80) cc_final: 0.9041 (m-80) REVERT: C 295 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: E 276 MET cc_start: 0.9192 (ttp) cc_final: 0.8975 (ttp) REVERT: F 276 MET cc_start: 0.9394 (ttp) cc_final: 0.8837 (tmm) REVERT: F 295 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.7172 (m-80) REVERT: J 261 ASN cc_start: 0.9312 (m-40) cc_final: 0.8940 (m-40) REVERT: J 266 TYR cc_start: 0.9458 (m-80) cc_final: 0.8866 (m-80) REVERT: K 272 ASN cc_start: 0.6491 (t0) cc_final: 0.6214 (p0) REVERT: K 284 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8292 (ttm170) REVERT: L 272 ASN cc_start: 0.6556 (t0) cc_final: 0.6296 (p0) REVERT: L 276 MET cc_start: 0.8750 (ttp) cc_final: 0.7134 (tpt) REVERT: L 295 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.7359 (m-80) outliers start: 36 outliers final: 26 residues processed: 144 average time/residue: 0.1290 time to fit residues: 23.5217 Evaluate side-chains 154 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 284 ARG Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 270 SER Chi-restraints excluded: chain L residue 295 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 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 = 0.4263 r_free = 0.4263 target = 0.134729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.123925 restraints weight = 7040.954| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 2.79 r_work: 0.4069 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3900 Z= 0.175 Angle : 0.488 3.385 5184 Z= 0.278 Chirality : 0.030 0.085 348 Planarity : 0.003 0.015 780 Dihedral : 4.142 12.680 588 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 8.91 % Allowed : 24.14 % Favored : 66.95 % 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: -3.65 (0.21), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.16), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.003 PHE E 281 TYR 0.017 0.002 TYR D 260 ARG 0.003 0.001 ARG J 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.475 Fit side-chains REVERT: A 289 TYR cc_start: 0.8988 (m-80) cc_final: 0.6734 (p90) REVERT: A 295 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: B 259 SER cc_start: 0.7581 (OUTLIER) cc_final: 0.6710 (p) REVERT: B 289 TYR cc_start: 0.8833 (m-80) cc_final: 0.6839 (p90) REVERT: C 261 ASN cc_start: 0.9334 (m-40) cc_final: 0.9127 (m-40) REVERT: C 266 TYR cc_start: 0.9227 (m-80) cc_final: 0.8922 (m-80) REVERT: D 263 PHE cc_start: 0.9155 (p90) cc_final: 0.8634 (p90) REVERT: D 276 MET cc_start: 0.9479 (ttp) cc_final: 0.9019 (tmm) REVERT: E 262 ASP cc_start: 0.8786 (t0) cc_final: 0.8506 (t0) REVERT: F 276 MET cc_start: 0.9432 (ttp) cc_final: 0.8764 (tmm) REVERT: F 295 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: G 263 PHE cc_start: 0.9206 (p90) cc_final: 0.9005 (p90) REVERT: I 276 MET cc_start: 0.8999 (ttp) cc_final: 0.8231 (tmm) REVERT: J 261 ASN cc_start: 0.9241 (m-40) cc_final: 0.8875 (m-40) REVERT: J 266 TYR cc_start: 0.9387 (m-80) cc_final: 0.8971 (m-80) REVERT: K 266 TYR cc_start: 0.9047 (m-80) cc_final: 0.8777 (m-80) REVERT: K 284 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8791 (ttm-80) REVERT: L 272 ASN cc_start: 0.6467 (t0) cc_final: 0.6170 (p0) REVERT: L 276 MET cc_start: 0.8465 (ttp) cc_final: 0.7001 (tpt) REVERT: L 280 ASN cc_start: 0.7479 (p0) cc_final: 0.6211 (t0) outliers start: 31 outliers final: 22 residues processed: 144 average time/residue: 0.1301 time to fit residues: 23.9632 Evaluate side-chains 153 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 270 SER Chi-restraints excluded: chain I residue 295 TYR Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 284 ARG Chi-restraints excluded: chain K residue 295 TYR Chi-restraints excluded: chain L residue 252 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 0.0030 chunk 0 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 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 = 0.4272 r_free = 0.4272 target = 0.134482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.123666 restraints weight = 6939.955| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 2.81 r_work: 0.4074 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3900 Z= 0.184 Angle : 0.491 3.274 5184 Z= 0.281 Chirality : 0.030 0.086 348 Planarity : 0.003 0.021 780 Dihedral : 4.037 11.861 588 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 9.20 % Allowed : 23.28 % Favored : 67.53 % 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: -3.57 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.003 PHE F 281 TYR 0.019 0.002 TYR D 260 ARG 0.003 0.001 ARG J 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.445 Fit side-chains REVERT: A 295 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: B 259 SER cc_start: 0.7438 (OUTLIER) cc_final: 0.6545 (p) REVERT: C 276 MET cc_start: 0.8844 (tmm) cc_final: 0.8619 (tmm) REVERT: C 295 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: D 263 PHE cc_start: 0.9163 (p90) cc_final: 0.8626 (p90) REVERT: D 276 MET cc_start: 0.9446 (ttp) cc_final: 0.8852 (tmm) REVERT: F 276 MET cc_start: 0.9354 (ttp) cc_final: 0.8309 (ttp) REVERT: F 295 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: G 263 PHE cc_start: 0.9171 (p90) cc_final: 0.8951 (p90) REVERT: G 276 MET cc_start: 0.9288 (ttp) cc_final: 0.8939 (ttp) REVERT: I 276 MET cc_start: 0.8931 (ttp) cc_final: 0.8294 (tmm) REVERT: J 261 ASN cc_start: 0.9248 (m-40) cc_final: 0.8857 (m-40) REVERT: J 266 TYR cc_start: 0.9407 (m-80) cc_final: 0.9076 (m-80) REVERT: K 260 TYR cc_start: 0.8634 (t80) cc_final: 0.8315 (t80) REVERT: K 266 TYR cc_start: 0.9051 (m-80) cc_final: 0.8736 (m-80) REVERT: K 284 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8809 (ttm-80) REVERT: L 276 MET cc_start: 0.8393 (ttp) cc_final: 0.7332 (tpt) REVERT: L 280 ASN cc_start: 0.7240 (p0) cc_final: 0.6032 (t0) REVERT: L 295 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.7326 (m-80) outliers start: 32 outliers final: 24 residues processed: 139 average time/residue: 0.1265 time to fit residues: 22.5654 Evaluate side-chains 151 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 270 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 284 ARG Chi-restraints excluded: chain K residue 295 TYR Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 295 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 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 = 0.4148 r_free = 0.4148 target = 0.125614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.114871 restraints weight = 7187.614| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.73 r_work: 0.3957 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.036 3900 Z= 0.398 Angle : 0.592 4.349 5184 Z= 0.338 Chirality : 0.032 0.093 348 Planarity : 0.004 0.025 780 Dihedral : 4.886 13.380 588 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 10.34 % Allowed : 23.85 % Favored : 65.80 % 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: -3.65 (0.21), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.16), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.029 0.004 PHE F 281 TYR 0.037 0.003 TYR E 266 ARG 0.003 0.001 ARG J 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.428 Fit side-chains REVERT: A 295 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: B 259 SER cc_start: 0.7523 (OUTLIER) cc_final: 0.6449 (p) REVERT: C 266 TYR cc_start: 0.9413 (m-80) cc_final: 0.8865 (m-80) REVERT: C 295 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: D 262 ASP cc_start: 0.8926 (t0) cc_final: 0.8716 (t0) REVERT: D 263 PHE cc_start: 0.9356 (p90) cc_final: 0.8930 (p90) REVERT: F 276 MET cc_start: 0.9357 (ttp) cc_final: 0.8383 (ttp) REVERT: F 295 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.7654 (m-80) REVERT: G 276 MET cc_start: 0.9338 (ttp) cc_final: 0.8905 (ttp) REVERT: I 276 MET cc_start: 0.9001 (ttp) cc_final: 0.8250 (tmm) REVERT: J 261 ASN cc_start: 0.9320 (m-40) cc_final: 0.8962 (m-40) REVERT: J 266 TYR cc_start: 0.9465 (m-80) cc_final: 0.9066 (m-80) REVERT: K 284 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8132 (ttm170) REVERT: L 295 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.7395 (m-80) outliers start: 36 outliers final: 27 residues processed: 128 average time/residue: 0.1246 time to fit residues: 20.4826 Evaluate side-chains 139 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 260 TYR Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 252 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 265 ASN Chi-restraints excluded: chain K residue 284 ARG Chi-restraints excluded: chain K residue 295 TYR Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 286 SER Chi-restraints excluded: chain L residue 295 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 ASN ** F 261 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 = 0.4296 r_free = 0.4296 target = 0.135832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.124935 restraints weight = 6865.871| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 2.84 r_work: 0.4094 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3900 Z= 0.159 Angle : 0.499 3.825 5184 Z= 0.286 Chirality : 0.032 0.099 348 Planarity : 0.003 0.026 780 Dihedral : 4.086 13.793 588 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 8.33 % Allowed : 26.72 % Favored : 64.94 % 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: -3.58 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.003 PHE F 281 TYR 0.020 0.002 TYR D 260 ARG 0.003 0.001 ARG J 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.411 Fit side-chains REVERT: A 273 PHE cc_start: 0.8499 (t80) cc_final: 0.8247 (t80) REVERT: A 295 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: B 259 SER cc_start: 0.7255 (OUTLIER) cc_final: 0.6269 (p) REVERT: B 289 TYR cc_start: 0.8865 (m-80) cc_final: 0.6847 (p90) REVERT: C 263 PHE cc_start: 0.9239 (p90) cc_final: 0.8991 (p90) REVERT: C 266 TYR cc_start: 0.9365 (m-80) cc_final: 0.9046 (m-80) REVERT: C 295 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: D 263 PHE cc_start: 0.9244 (p90) cc_final: 0.8848 (p90) REVERT: F 276 MET cc_start: 0.9293 (ttp) cc_final: 0.7891 (ttp) REVERT: G 263 PHE cc_start: 0.9175 (p90) cc_final: 0.8929 (p90) REVERT: H 276 MET cc_start: 0.9152 (ttp) cc_final: 0.7894 (ttp) REVERT: I 276 MET cc_start: 0.9006 (ttp) cc_final: 0.8641 (tmm) REVERT: J 259 SER cc_start: 0.9238 (m) cc_final: 0.8773 (p) REVERT: J 261 ASN cc_start: 0.9201 (m-40) cc_final: 0.8940 (m-40) REVERT: J 266 TYR cc_start: 0.9402 (m-80) cc_final: 0.9120 (m-80) REVERT: K 260 TYR cc_start: 0.8637 (t80) cc_final: 0.8383 (t80) REVERT: K 266 TYR cc_start: 0.8994 (m-80) cc_final: 0.8518 (m-80) REVERT: K 280 ASN cc_start: 0.7182 (p0) cc_final: 0.5947 (t0) REVERT: K 284 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8879 (ttm-80) REVERT: L 276 MET cc_start: 0.8295 (ttp) cc_final: 0.7243 (tpt) REVERT: L 280 ASN cc_start: 0.7162 (p0) cc_final: 0.6044 (t0) REVERT: L 295 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.7287 (m-80) outliers start: 29 outliers final: 21 residues processed: 132 average time/residue: 0.1223 time to fit residues: 20.9647 Evaluate side-chains 140 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 252 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 284 ARG Chi-restraints excluded: chain K residue 295 TYR Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 270 SER Chi-restraints excluded: chain L residue 295 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN ** F 261 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 = 0.4337 r_free = 0.4337 target = 0.139347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.128295 restraints weight = 6845.723| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.90 r_work: 0.4128 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3900 Z= 0.146 Angle : 0.483 3.784 5184 Z= 0.278 Chirality : 0.031 0.096 348 Planarity : 0.003 0.020 780 Dihedral : 3.851 13.513 588 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 7.76 % Allowed : 26.15 % Favored : 66.09 % 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: -3.55 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.003 PHE F 281 TYR 0.019 0.002 TYR D 260 ARG 0.003 0.001 ARG J 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.327 Fit side-chains REVERT: A 295 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7620 (m-80) REVERT: B 259 SER cc_start: 0.6739 (OUTLIER) cc_final: 0.5708 (p) REVERT: B 284 ARG cc_start: 0.8355 (ttt180) cc_final: 0.4842 (mpt180) REVERT: B 289 TYR cc_start: 0.8882 (m-80) cc_final: 0.6869 (p90) REVERT: C 263 PHE cc_start: 0.9249 (p90) cc_final: 0.9002 (p90) REVERT: C 266 TYR cc_start: 0.9361 (m-80) cc_final: 0.9124 (m-80) REVERT: C 295 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.7398 (m-80) REVERT: D 263 PHE cc_start: 0.9205 (p90) cc_final: 0.8861 (p90) REVERT: F 265 ASN cc_start: 0.9203 (m-40) cc_final: 0.9002 (m-40) REVERT: F 276 MET cc_start: 0.9290 (ttp) cc_final: 0.7882 (ttp) REVERT: G 252 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.8338 (p) REVERT: G 263 PHE cc_start: 0.9152 (p90) cc_final: 0.8916 (p90) REVERT: G 266 TYR cc_start: 0.9423 (m-80) cc_final: 0.9143 (m-80) REVERT: H 276 MET cc_start: 0.9185 (ttp) cc_final: 0.8016 (ttp) REVERT: I 266 TYR cc_start: 0.9225 (m-80) cc_final: 0.8981 (m-80) REVERT: I 276 MET cc_start: 0.8938 (ttp) cc_final: 0.8645 (tmm) REVERT: J 252 SER cc_start: 0.8475 (OUTLIER) cc_final: 0.8138 (p) REVERT: J 261 ASN cc_start: 0.9153 (m-40) cc_final: 0.8834 (m-40) REVERT: J 266 TYR cc_start: 0.9388 (m-80) cc_final: 0.9133 (m-80) REVERT: J 280 ASN cc_start: 0.8723 (p0) cc_final: 0.8520 (p0) REVERT: J 284 ARG cc_start: 0.8866 (ttm-80) cc_final: 0.8653 (ttm-80) REVERT: K 260 TYR cc_start: 0.8666 (t80) cc_final: 0.8416 (t80) REVERT: K 266 TYR cc_start: 0.8970 (m-80) cc_final: 0.8382 (m-80) REVERT: K 280 ASN cc_start: 0.6640 (p0) cc_final: 0.5432 (t0) REVERT: L 276 MET cc_start: 0.8090 (ttp) cc_final: 0.7091 (tpt) REVERT: L 280 ASN cc_start: 0.6311 (p0) cc_final: 0.5522 (t0) REVERT: L 281 PHE cc_start: 0.7073 (m-80) cc_final: 0.5516 (p90) REVERT: L 295 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.7319 (m-80) outliers start: 27 outliers final: 20 residues processed: 132 average time/residue: 0.1342 time to fit residues: 22.6064 Evaluate side-chains 146 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 252 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 295 TYR Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 270 SER Chi-restraints excluded: chain L residue 295 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 261 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 = 0.4335 r_free = 0.4335 target = 0.139374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.128529 restraints weight = 6739.375| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.84 r_work: 0.4125 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 3900 Z= 0.244 Angle : 1.197 59.200 5184 Z= 0.734 Chirality : 0.031 0.105 348 Planarity : 0.003 0.022 780 Dihedral : 3.931 22.955 588 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 7.47 % Allowed : 27.01 % Favored : 65.52 % Cbeta Deviations : 0.29 % 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: -3.55 (0.23), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.003 PHE F 281 TYR 0.028 0.002 TYR B 260 ARG 0.004 0.001 ARG K 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1902.19 seconds wall clock time: 34 minutes 40.56 seconds (2080.56 seconds total)