Starting phenix.real_space_refine on Wed Mar 5 21:52:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zj2_14739/03_2025/7zj2_14739.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zj2_14739/03_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_14739/03_2025/7zj2_14739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zj2_14739/03_2025/7zj2_14739.map" model { file = "/net/cci-nas-00/data/ceres_data/7zj2_14739/03_2025/7zj2_14739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zj2_14739/03_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-5624/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: 0.97 Conformation dependent library (CDL) restraints added in 647.5 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: 0.30 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: 1.10 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: 1.090 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 11.930 Find NCS groups from input model: 0.100 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.380 ------------------------------------------------------------------------------- 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 : 0.420 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: 0.1627 time to fit residues: 47.5207 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 : 0.448 ------------------------------------------------------------------------------- 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 = 0.133401 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: 0.7292 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 : 0.430 Fit side-chains REVERT: A 263 PHE cc_start: 0.8737 (p90) cc_final: 0.6898 (m-10) REVERT: A 284 ARG cc_start: 0.8681 (ttt180) cc_final: 0.5411 (mtt90) REVERT: A 289 TYR cc_start: 0.9060 (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: 0.8708 (m-80) cc_final: 0.7993 (m-80) REVERT: B 289 TYR cc_start: 0.8885 (m-80) cc_final: 0.6895 (p90) REVERT: C 252 SER cc_start: 0.8381 (m) cc_final: 0.8062 (m) REVERT: C 260 TYR cc_start: 0.8278 (t80) cc_final: 0.8072 (t80) REVERT: C 263 PHE cc_start: 0.9123 (p90) cc_final: 0.8696 (p90) REVERT: D 276 MET cc_start: 0.9459 (ttp) cc_final: 0.9236 (tmm) REVERT: E 266 TYR cc_start: 0.9334 (m-80) cc_final: 0.8745 (m-80) REVERT: F 276 MET cc_start: 0.9265 (ttp) cc_final: 0.8972 (ttp) REVERT: H 276 MET cc_start: 0.9012 (ttp) cc_final: 0.8809 (tmm) REVERT: I 263 PHE cc_start: 0.9105 (p90) cc_final: 0.8603 (p90) REVERT: I 276 MET cc_start: 0.9010 (ttp) cc_final: 0.7983 (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: 0.8923 (p90) REVERT: J 266 TYR cc_start: 0.9269 (m-80) cc_final: 0.8931 (m-80) REVERT: J 276 MET cc_start: 0.9024 (ttp) cc_final: 0.7995 (ttp) REVERT: K 260 TYR cc_start: 0.8478 (t80) cc_final: 0.8256 (t80) REVERT: K 276 MET cc_start: 0.9149 (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: 0.8767 (m-80) REVERT: L 280 ASN cc_start: 0.8193 (p0) cc_final: 0.6709 (m-40) REVERT: L 281 PHE cc_start: 0.7466 (m-80) cc_final: 0.6956 (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: 0.1291 time to fit residues: 27.2852 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 : 0.403 ------------------------------------------------------------------------------- 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: 1.9990 chunk 16 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.137066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.126373 restraints weight = 6790.875| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 2.80 r_work: 0.4087 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3900 Z= 0.225 Angle : 0.541 4.174 5184 Z= 0.313 Chirality : 0.030 0.088 348 Planarity : 0.004 0.027 780 Dihedral : 4.644 10.930 588 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.76 % Allowed : 23.85 % Favored : 68.39 % 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: -3.62 (0.23), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.18), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.044 0.003 PHE L 263 TYR 0.018 0.002 TYR A 260 ARG 0.004 0.001 ARG F 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 172 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 289 TYR cc_start: 0.9014 (m-80) cc_final: 0.7064 (p90) REVERT: A 295 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: B 259 SER cc_start: 0.7156 (OUTLIER) cc_final: 0.6172 (p) REVERT: C 261 ASN cc_start: 0.9395 (m-40) cc_final: 0.9070 (m-40) REVERT: C 263 PHE cc_start: 0.9289 (p90) cc_final: 0.8990 (p90) REVERT: D 276 MET cc_start: 0.9499 (ttp) cc_final: 0.8810 (tmm) REVERT: F 259 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8559 (p) REVERT: F 295 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.6877 (m-80) REVERT: G 263 PHE cc_start: 0.9238 (p90) cc_final: 0.8976 (p90) REVERT: G 276 MET cc_start: 0.9362 (ttp) cc_final: 0.8562 (tmm) REVERT: H 266 TYR cc_start: 0.9373 (m-80) cc_final: 0.9171 (m-80) REVERT: J 252 SER cc_start: 0.8479 (m) cc_final: 0.8190 (p) REVERT: J 261 ASN cc_start: 0.9382 (m-40) cc_final: 0.8987 (m-40) REVERT: J 266 TYR cc_start: 0.9205 (m-80) cc_final: 0.8818 (m-80) REVERT: J 276 MET cc_start: 0.8787 (ttp) cc_final: 0.7265 (ttt) REVERT: K 280 ASN cc_start: 0.8101 (p0) cc_final: 0.6596 (t0) REVERT: L 272 ASN cc_start: 0.6990 (t0) cc_final: 0.6422 (p0) REVERT: L 276 MET cc_start: 0.8327 (ttp) cc_final: 0.6936 (tpt) outliers start: 27 outliers final: 22 residues processed: 156 average time/residue: 0.1261 time to fit residues: 24.9939 Evaluate side-chains 162 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 281 PHE 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: 5.9990 chunk 6 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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 = 0.4351 r_free = 0.4351 target = 0.142023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.131043 restraints weight = 6686.658| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.94 r_work: 0.4152 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.5497 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= 0.157 Angle : 0.495 3.405 5184 Z= 0.283 Chirality : 0.030 0.091 348 Planarity : 0.003 0.022 780 Dihedral : 4.121 11.617 588 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 8.05 % Allowed : 25.57 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.59 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (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 G 260 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 167 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.379 Fit side-chains REVERT: A 289 TYR cc_start: 0.9056 (m-80) cc_final: 0.7047 (p90) REVERT: A 295 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: B 259 SER cc_start: 0.7141 (OUTLIER) cc_final: 0.6188 (p) REVERT: B 276 MET cc_start: 0.7896 (tpp) cc_final: 0.7404 (mtt) REVERT: B 289 TYR cc_start: 0.8825 (m-80) cc_final: 0.6966 (p90) REVERT: C 260 TYR cc_start: 0.8257 (t80) cc_final: 0.7931 (t80) REVERT: C 263 PHE cc_start: 0.9217 (p90) cc_final: 0.8933 (p90) REVERT: D 260 TYR cc_start: 0.8575 (t80) cc_final: 0.8319 (t80) REVERT: D 276 MET cc_start: 0.9390 (ttp) cc_final: 0.8814 (tmm) REVERT: F 276 MET cc_start: 0.9454 (ttp) cc_final: 0.8281 (ttp) REVERT: F 295 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.6871 (m-80) REVERT: G 263 PHE cc_start: 0.9237 (p90) cc_final: 0.9036 (p90) REVERT: H 266 TYR cc_start: 0.9364 (m-80) cc_final: 0.9083 (m-80) REVERT: H 276 MET cc_start: 0.9214 (tpt) cc_final: 0.8861 (tpp) REVERT: I 266 TYR cc_start: 0.9221 (m-80) cc_final: 0.8891 (m-80) REVERT: I 276 MET cc_start: 0.8718 (ttp) cc_final: 0.8049 (ppp) REVERT: J 252 SER cc_start: 0.8361 (m) cc_final: 0.8109 (p) REVERT: J 261 ASN cc_start: 0.9279 (m-40) cc_final: 0.8901 (m-40) REVERT: J 266 TYR cc_start: 0.9273 (m-80) cc_final: 0.8625 (m-80) REVERT: J 276 MET cc_start: 0.8738 (ttp) cc_final: 0.8460 (ttp) REVERT: K 260 TYR cc_start: 0.8567 (t80) cc_final: 0.8281 (t80) REVERT: K 280 ASN cc_start: 0.7595 (p0) cc_final: 0.6329 (t0) REVERT: L 272 ASN cc_start: 0.6610 (t0) cc_final: 0.6329 (p0) REVERT: L 276 MET cc_start: 0.8361 (ttp) cc_final: 0.7899 (ppp) REVERT: L 280 ASN cc_start: 0.7286 (p0) cc_final: 0.6234 (t0) outliers start: 28 outliers final: 20 residues processed: 147 average time/residue: 0.1220 time to fit residues: 23.0226 Evaluate side-chains 152 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 I residue 270 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.136261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.125423 restraints weight = 6959.655| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.83 r_work: 0.4001 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 3900 Z= 0.324 Angle : 0.560 3.570 5184 Z= 0.318 Chirality : 0.031 0.085 348 Planarity : 0.004 0.030 780 Dihedral : 4.805 13.702 588 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 8.62 % Allowed : 23.85 % 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: -3.66 (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 0.028 0.004 PHE G 281 TYR 0.032 0.002 TYR C 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 152 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.433 Fit side-chains REVERT: A 295 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7675 (m-80) REVERT: B 272 ASN cc_start: 0.8943 (p0) cc_final: 0.8616 (p0) REVERT: B 276 MET cc_start: 0.8280 (tpp) cc_final: 0.7802 (mtt) REVERT: C 295 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: D 263 PHE cc_start: 0.9198 (p90) cc_final: 0.8809 (p90) REVERT: D 276 MET cc_start: 0.9444 (ttp) cc_final: 0.8966 (tmm) REVERT: F 276 MET cc_start: 0.9368 (ttp) cc_final: 0.8387 (ttp) REVERT: F 295 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.6897 (m-80) REVERT: H 276 MET cc_start: 0.9200 (tpt) cc_final: 0.8794 (tpp) REVERT: J 252 SER cc_start: 0.8594 (m) cc_final: 0.8248 (p) REVERT: J 261 ASN cc_start: 0.9340 (m-40) cc_final: 0.8936 (m-40) REVERT: J 266 TYR cc_start: 0.9426 (m-80) cc_final: 0.8945 (m-80) REVERT: J 276 MET cc_start: 0.8864 (ttp) cc_final: 0.8608 (ttp) REVERT: L 263 PHE cc_start: 0.7549 (p90) cc_final: 0.7325 (p90) REVERT: L 272 ASN cc_start: 0.6814 (t0) cc_final: 0.6593 (p0) REVERT: L 295 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.7301 (m-80) outliers start: 30 outliers final: 21 residues processed: 137 average time/residue: 0.1183 time to fit residues: 20.8445 Evaluate side-chains 141 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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** ** G 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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 = 0.4372 r_free = 0.4372 target = 0.142903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.132463 restraints weight = 6697.974| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 2.78 r_work: 0.4116 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3900 Z= 0.186 Angle : 0.490 3.336 5184 Z= 0.277 Chirality : 0.030 0.085 348 Planarity : 0.003 0.029 780 Dihedral : 4.179 12.422 588 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 9.48 % Allowed : 22.70 % 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: -3.59 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.16), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.028 0.003 PHE E 281 TYR 0.018 0.002 TYR D 260 ARG 0.003 0.001 ARG C 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 163 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.415 Fit side-chains REVERT: A 295 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7530 (m-80) REVERT: B 276 MET cc_start: 0.7657 (tpp) cc_final: 0.7377 (mtt) REVERT: B 289 TYR cc_start: 0.8842 (m-80) cc_final: 0.6847 (p90) REVERT: C 263 PHE cc_start: 0.9231 (p90) cc_final: 0.8977 (p90) REVERT: C 295 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.7326 (m-80) REVERT: D 276 MET cc_start: 0.9469 (ttp) cc_final: 0.8994 (tmm) REVERT: F 276 MET cc_start: 0.9398 (ttp) cc_final: 0.8349 (ttp) REVERT: F 295 TYR cc_start: 0.7800 (OUTLIER) cc_final: 0.7129 (m-80) REVERT: H 262 ASP cc_start: 0.8695 (t0) cc_final: 0.8431 (t0) REVERT: H 276 MET cc_start: 0.9190 (tpt) cc_final: 0.8581 (tpt) REVERT: I 277 LYS cc_start: 0.6507 (tttt) cc_final: 0.6303 (tttt) REVERT: J 252 SER cc_start: 0.8420 (m) cc_final: 0.8073 (p) REVERT: J 261 ASN cc_start: 0.9239 (m-40) cc_final: 0.8869 (m-40) REVERT: J 266 TYR cc_start: 0.9357 (m-80) cc_final: 0.8848 (m-80) REVERT: J 276 MET cc_start: 0.8602 (ttp) cc_final: 0.7704 (ttp) REVERT: K 266 TYR cc_start: 0.9003 (m-80) cc_final: 0.8643 (m-80) REVERT: K 284 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8813 (ttm-80) REVERT: L 263 PHE cc_start: 0.7530 (p90) cc_final: 0.7296 (p90) REVERT: L 272 ASN cc_start: 0.6760 (t0) cc_final: 0.6405 (p0) REVERT: L 276 MET cc_start: 0.8068 (ttp) cc_final: 0.6899 (tpt) REVERT: L 280 ASN cc_start: 0.7440 (p0) cc_final: 0.6236 (t0) REVERT: L 295 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.7365 (m-80) outliers start: 33 outliers final: 23 residues processed: 144 average time/residue: 0.1362 time to fit residues: 24.7697 Evaluate side-chains 151 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 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 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 270 SER Chi-restraints excluded: chain K residue 284 ARG Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 295 TYR 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: 0.8980 chunk 39 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 0 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.144229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.132821 restraints weight = 7152.346| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.89 r_work: 0.4197 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3900 Z= 0.150 Angle : 0.476 3.127 5184 Z= 0.273 Chirality : 0.030 0.084 348 Planarity : 0.003 0.027 780 Dihedral : 3.929 12.372 588 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 7.76 % Allowed : 23.56 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.52 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.003 PHE F 281 TYR 0.026 0.002 TYR E 266 ARG 0.003 0.001 ARG C 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 152 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.433 Fit side-chains REVERT: A 295 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7475 (m-80) REVERT: B 276 MET cc_start: 0.7702 (tpp) cc_final: 0.7455 (mtt) REVERT: C 263 PHE cc_start: 0.9294 (p90) cc_final: 0.9030 (p90) REVERT: C 266 TYR cc_start: 0.9199 (m-80) cc_final: 0.8915 (m-80) REVERT: C 295 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.7310 (m-80) REVERT: D 276 MET cc_start: 0.9450 (ttp) cc_final: 0.8984 (tmm) REVERT: F 276 MET cc_start: 0.9391 (ttp) cc_final: 0.8412 (ttp) REVERT: F 295 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: H 276 MET cc_start: 0.9185 (tpt) cc_final: 0.8929 (tpp) REVERT: I 276 MET cc_start: 0.8790 (ttp) cc_final: 0.8348 (tmm) REVERT: J 252 SER cc_start: 0.8439 (m) cc_final: 0.8094 (p) REVERT: J 261 ASN cc_start: 0.9217 (m-40) cc_final: 0.8886 (m-40) REVERT: J 266 TYR cc_start: 0.9356 (m-80) cc_final: 0.8938 (m-80) REVERT: J 276 MET cc_start: 0.8655 (ttp) cc_final: 0.8366 (ttp) REVERT: K 260 TYR cc_start: 0.8624 (t80) cc_final: 0.8281 (t80) REVERT: K 266 TYR cc_start: 0.9005 (m-80) cc_final: 0.8510 (m-80) REVERT: K 280 ASN cc_start: 0.6941 (p0) cc_final: 0.5523 (t0) REVERT: K 281 PHE cc_start: 0.6474 (m-80) cc_final: 0.5945 (m-10) REVERT: L 272 ASN cc_start: 0.6389 (t0) cc_final: 0.6156 (p0) REVERT: L 276 MET cc_start: 0.7975 (ttp) cc_final: 0.6743 (tpt) REVERT: L 280 ASN cc_start: 0.6795 (p0) cc_final: 0.5995 (t0) REVERT: L 295 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7412 (m-80) outliers start: 27 outliers final: 21 residues processed: 136 average time/residue: 0.1263 time to fit residues: 21.8761 Evaluate side-chains 144 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 295 TYR 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 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 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: 4.9990 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.140632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.129498 restraints weight = 6735.499| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.86 r_work: 0.4132 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.5944 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= 0.233 Angle : 0.509 3.273 5184 Z= 0.291 Chirality : 0.030 0.088 348 Planarity : 0.003 0.021 780 Dihedral : 4.194 13.164 588 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 7.76 % Allowed : 23.28 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.53 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.003 PHE F 281 TYR 0.018 0.002 TYR H 260 ARG 0.002 0.000 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 145 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.387 Fit side-chains REVERT: A 295 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: C 295 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.7361 (m-80) REVERT: D 263 PHE cc_start: 0.9057 (p90) cc_final: 0.8778 (p90) REVERT: D 276 MET cc_start: 0.9436 (ttp) cc_final: 0.8868 (tmm) REVERT: E 259 SER cc_start: 0.9047 (OUTLIER) cc_final: 0.8496 (p) REVERT: F 276 MET cc_start: 0.9388 (ttp) cc_final: 0.8376 (ttp) REVERT: F 295 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: I 276 MET cc_start: 0.8804 (ttp) cc_final: 0.8332 (tmm) REVERT: J 252 SER cc_start: 0.8563 (m) cc_final: 0.8193 (p) REVERT: J 261 ASN cc_start: 0.9286 (m-40) cc_final: 0.8913 (m-40) REVERT: J 266 TYR cc_start: 0.9430 (m-80) cc_final: 0.8970 (m-80) REVERT: J 276 MET cc_start: 0.8750 (ttp) cc_final: 0.8249 (ttt) REVERT: K 266 TYR cc_start: 0.9015 (m-80) cc_final: 0.8563 (m-80) REVERT: L 272 ASN cc_start: 0.6448 (t0) cc_final: 0.6161 (p0) REVERT: L 276 MET cc_start: 0.8307 (ttp) cc_final: 0.7003 (tpt) REVERT: L 280 ASN cc_start: 0.7288 (p0) cc_final: 0.6043 (t0) REVERT: L 295 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7411 (m-80) outliers start: 27 outliers final: 21 residues processed: 130 average time/residue: 0.1224 time to fit residues: 20.5750 Evaluate side-chains 141 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 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 J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain L residue 252 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: 2.9990 chunk 33 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 268 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 = 0.4256 r_free = 0.4256 target = 0.132443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.121681 restraints weight = 6932.555| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.77 r_work: 0.4092 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 3900 Z= 0.262 Angle : 0.538 3.816 5184 Z= 0.306 Chirality : 0.031 0.096 348 Planarity : 0.003 0.020 780 Dihedral : 4.363 15.657 588 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 7.47 % Allowed : 23.56 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 : -2.72 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.003 PHE F 281 TYR 0.018 0.002 TYR H 260 ARG 0.002 0.000 ARG K 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 139 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.395 Fit side-chains REVERT: A 295 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: C 295 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: D 276 MET cc_start: 0.9458 (ttp) cc_final: 0.8753 (tmm) REVERT: E 259 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8527 (p) REVERT: F 276 MET cc_start: 0.9342 (ttp) cc_final: 0.8603 (ttp) REVERT: I 276 MET cc_start: 0.8676 (ttp) cc_final: 0.8243 (tmm) REVERT: J 261 ASN cc_start: 0.9299 (m-40) cc_final: 0.8919 (m-40) REVERT: J 266 TYR cc_start: 0.9451 (m-80) cc_final: 0.8883 (m-80) REVERT: K 266 TYR cc_start: 0.9060 (m-80) cc_final: 0.8688 (m-80) REVERT: K 276 MET cc_start: 0.8287 (ttp) cc_final: 0.7567 (ppp) REVERT: K 280 ASN cc_start: 0.7463 (p0) cc_final: 0.6021 (t0) REVERT: L 276 MET cc_start: 0.8462 (ttp) cc_final: 0.7577 (tpt) REVERT: L 295 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.7371 (m-80) outliers start: 26 outliers final: 20 residues processed: 125 average time/residue: 0.1198 time to fit residues: 19.3444 Evaluate side-chains 137 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 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 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain L residue 252 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: 4.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.144511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.132609 restraints weight = 7027.263| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.80 r_work: 0.4163 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3900 Z= 0.144 Angle : 0.497 4.056 5184 Z= 0.283 Chirality : 0.032 0.099 348 Planarity : 0.003 0.020 780 Dihedral : 3.898 15.002 588 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 6.32 % Allowed : 25.29 % Favored : 68.39 % 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: -3.59 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.002 PHE F 281 TYR 0.020 0.002 TYR H 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 146 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.384 Fit side-chains REVERT: A 289 TYR cc_start: 0.9022 (m-80) cc_final: 0.6773 (p90) REVERT: A 295 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: B 259 SER cc_start: 0.7434 (OUTLIER) cc_final: 0.6484 (p) REVERT: B 289 TYR cc_start: 0.8861 (m-80) cc_final: 0.6852 (p90) REVERT: C 263 PHE cc_start: 0.9252 (p90) cc_final: 0.9036 (p90) REVERT: C 295 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: D 263 PHE cc_start: 0.9046 (p90) cc_final: 0.8724 (p90) REVERT: D 276 MET cc_start: 0.9433 (ttp) cc_final: 0.8902 (tmm) REVERT: F 276 MET cc_start: 0.9067 (ttp) cc_final: 0.8539 (tmm) REVERT: G 252 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8368 (p) REVERT: G 276 MET cc_start: 0.9248 (ttp) cc_final: 0.8966 (ttp) REVERT: H 260 TYR cc_start: 0.8551 (t80) cc_final: 0.8298 (t80) REVERT: I 276 MET cc_start: 0.8673 (ttp) cc_final: 0.8399 (tmm) REVERT: J 261 ASN cc_start: 0.9196 (m-40) cc_final: 0.8919 (m-40) REVERT: J 266 TYR cc_start: 0.9417 (m-80) cc_final: 0.9019 (m-80) REVERT: K 260 TYR cc_start: 0.8675 (t80) cc_final: 0.8383 (t80) REVERT: K 266 TYR cc_start: 0.9045 (m-80) cc_final: 0.8562 (m-80) REVERT: K 276 MET cc_start: 0.7991 (ttp) cc_final: 0.7075 (tpt) REVERT: K 280 ASN cc_start: 0.6854 (p0) cc_final: 0.5702 (t0) REVERT: L 276 MET cc_start: 0.7951 (ttp) cc_final: 0.7270 (tpt) REVERT: L 280 ASN cc_start: 0.6849 (p0) cc_final: 0.5708 (t0) REVERT: L 281 PHE cc_start: 0.7183 (m-10) cc_final: 0.5475 (p90) REVERT: L 295 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.7304 (m-80) outliers start: 22 outliers final: 17 residues processed: 131 average time/residue: 0.1119 time to fit residues: 19.1055 Evaluate side-chains 142 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 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 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain L residue 252 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: 0.3980 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.138253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.127244 restraints weight = 6885.774| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.86 r_work: 0.4115 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3900 Z= 0.189 Angle : 0.503 3.853 5184 Z= 0.288 Chirality : 0.031 0.095 348 Planarity : 0.003 0.017 780 Dihedral : 3.967 15.173 588 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 6.32 % Allowed : 25.00 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.022 0.003 PHE F 281 TYR 0.020 0.002 TYR B 266 ARG 0.002 0.000 ARG C 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1939.05 seconds wall clock time: 34 minutes 20.85 seconds (2060.85 seconds total)