Starting phenix.real_space_refine on Mon Sep 23 16:09:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/09_2024/7zj2_14739.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/09_2024/7zj2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/09_2024/7zj2_14739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/09_2024/7zj2_14739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/09_2024/7zj2_14739.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/09_2024/7zj2_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-5461/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: 1.58, 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: 0.88 Conformation dependent library (CDL) restraints added in 474.8 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: 0.26 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: 1.02 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' 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: 1.320 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.700 Find NCS groups from input model: 0.130 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.020 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 0.365 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: 0.1576 time to fit residues: 45.7987 Evaluate side-chains 180 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 0.406 Fit side-chains REVERT: A 263 PHE cc_start: 0.8415 (p90) cc_final: 0.7009 (m-10) REVERT: A 284 ARG cc_start: 0.8673 (ttt180) cc_final: 0.5796 (mtt90) REVERT: A 289 TYR cc_start: 0.8722 (m-80) cc_final: 0.7056 (p90) REVERT: B 263 PHE cc_start: 0.8615 (p90) cc_final: 0.7066 (m-80) REVERT: B 266 TYR cc_start: 0.8311 (m-80) cc_final: 0.7829 (m-80) REVERT: B 289 TYR cc_start: 0.8540 (m-80) cc_final: 0.6945 (p90) REVERT: C 252 SER cc_start: 0.8439 (m) cc_final: 0.8169 (m) REVERT: C 263 PHE cc_start: 0.8505 (p90) cc_final: 0.8243 (p90) REVERT: E 266 TYR cc_start: 0.8615 (m-80) cc_final: 0.8056 (m-80) REVERT: I 263 PHE cc_start: 0.8544 (p90) cc_final: 0.8309 (p90) REVERT: I 276 MET cc_start: 0.7599 (ttp) cc_final: 0.7280 (ttp) REVERT: J 252 SER cc_start: 0.8365 (m) cc_final: 0.7882 (m) REVERT: J 276 MET cc_start: 0.7894 (ttp) cc_final: 0.7261 (ttp) REVERT: K 280 ASN cc_start: 0.8050 (p0) cc_final: 0.7386 (t0) REVERT: L 280 ASN cc_start: 0.8196 (p0) cc_final: 0.7071 (m-40) REVERT: L 281 PHE cc_start: 0.7546 (m-80) cc_final: 0.7208 (m-80) outliers start: 19 outliers final: 14 residues processed: 167 average time/residue: 0.1312 time to fit residues: 27.7615 Evaluate side-chains 156 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 24 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3900 Z= 0.290 Angle : 0.577 4.720 5184 Z= 0.331 Chirality : 0.031 0.089 348 Planarity : 0.004 0.028 780 Dihedral : 4.960 11.842 588 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.76 % Allowed : 24.43 % 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: -3.67 (0.23), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.042 0.003 PHE L 263 TYR 0.017 0.002 TYR C 260 ARG 0.005 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 162 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 0.402 Fit side-chains REVERT: A 262 ASP cc_start: 0.7613 (t0) cc_final: 0.7379 (t0) REVERT: A 289 TYR cc_start: 0.8743 (m-80) cc_final: 0.7050 (p90) REVERT: A 295 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7642 (m-80) REVERT: B 259 SER cc_start: 0.7944 (OUTLIER) cc_final: 0.7154 (p) REVERT: C 261 ASN cc_start: 0.8687 (m-40) cc_final: 0.8469 (m-40) REVERT: F 259 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8580 (p) REVERT: F 295 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: J 252 SER cc_start: 0.8495 (m) cc_final: 0.8214 (p) REVERT: J 261 ASN cc_start: 0.8705 (m-40) cc_final: 0.8405 (m-40) REVERT: L 276 MET cc_start: 0.7474 (ttp) cc_final: 0.7180 (tpt) outliers start: 27 outliers final: 21 residues processed: 146 average time/residue: 0.1211 time to fit residues: 22.4399 Evaluate side-chains 156 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5598 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= 0.123 Angle : 0.489 3.508 5184 Z= 0.282 Chirality : 0.031 0.082 348 Planarity : 0.003 0.021 780 Dihedral : 4.048 11.834 588 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -3.58 (0.23), 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 0.028 0.003 PHE F 281 TYR 0.018 0.002 TYR K 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 172 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 0.383 Fit side-chains REVERT: A 289 TYR cc_start: 0.8732 (m-80) cc_final: 0.7071 (p90) REVERT: A 295 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: B 259 SER cc_start: 0.7914 (OUTLIER) cc_final: 0.7134 (p) REVERT: B 289 TYR cc_start: 0.8552 (m-80) cc_final: 0.7080 (p90) REVERT: C 263 PHE cc_start: 0.8609 (p90) cc_final: 0.8393 (p90) REVERT: F 295 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7142 (m-80) REVERT: H 266 TYR cc_start: 0.8674 (m-80) cc_final: 0.8434 (m-80) REVERT: J 252 SER cc_start: 0.8418 (m) cc_final: 0.8143 (p) REVERT: L 280 ASN cc_start: 0.6718 (p0) cc_final: 0.6489 (t0) outliers start: 27 outliers final: 20 residues processed: 153 average time/residue: 0.1171 time to fit residues: 22.9639 Evaluate side-chains 151 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 ASN ** J 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 3900 Z= 0.295 Angle : 0.561 3.581 5184 Z= 0.322 Chirality : 0.031 0.080 348 Planarity : 0.004 0.029 780 Dihedral : 4.623 13.512 588 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 8.91 % Allowed : 22.99 % Favored : 68.10 % 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 : -2.79 (0.16), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.031 0.004 PHE G 281 TYR 0.032 0.002 TYR C 266 ARG 0.004 0.001 ARG C 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 157 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 0.417 Fit side-chains REVERT: A 295 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: C 295 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7670 (m-80) REVERT: E 295 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: F 295 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: J 252 SER cc_start: 0.8495 (m) cc_final: 0.8190 (p) REVERT: J 266 TYR cc_start: 0.8847 (m-80) cc_final: 0.8624 (m-80) REVERT: K 284 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8869 (ttm170) REVERT: L 263 PHE cc_start: 0.6997 (p90) cc_final: 0.6779 (p90) REVERT: L 295 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7456 (m-80) outliers start: 31 outliers final: 22 residues processed: 142 average time/residue: 0.1274 time to fit residues: 22.9232 Evaluate side-chains 150 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 281 PHE Chi-restraints excluded: chain E residue 295 TYR 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 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 271 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.6042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3900 Z= 0.156 Angle : 0.499 3.293 5184 Z= 0.287 Chirality : 0.031 0.087 348 Planarity : 0.003 0.026 780 Dihedral : 4.040 12.206 588 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 8.33 % Allowed : 22.41 % Favored : 69.25 % 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 0.023 0.002 TYR J 266 ARG 0.004 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 156 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 0.395 Fit side-chains REVERT: A 295 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: B 259 SER cc_start: 0.7728 (OUTLIER) cc_final: 0.7170 (p) REVERT: B 289 TYR cc_start: 0.8542 (m-80) cc_final: 0.7031 (p90) REVERT: C 263 PHE cc_start: 0.8701 (p90) cc_final: 0.8482 (p90) REVERT: C 295 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: F 295 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7376 (m-80) REVERT: J 252 SER cc_start: 0.8465 (m) cc_final: 0.8142 (p) REVERT: L 280 ASN cc_start: 0.7198 (p0) cc_final: 0.6376 (t0) REVERT: L 295 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7535 (m-80) outliers start: 29 outliers final: 19 residues processed: 139 average time/residue: 0.1147 time to fit residues: 20.6381 Evaluate side-chains 148 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 3900 Z= 0.240 Angle : 0.526 4.448 5184 Z= 0.300 Chirality : 0.030 0.084 348 Planarity : 0.003 0.024 780 Dihedral : 4.305 13.437 588 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 8.91 % Allowed : 22.70 % 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: -3.54 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.029 0.003 PHE H 263 TYR 0.034 0.002 TYR E 266 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 142 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 0.392 Fit side-chains REVERT: A 295 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: B 289 TYR cc_start: 0.8642 (m-80) cc_final: 0.6972 (p90) REVERT: C 295 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: E 295 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: F 295 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: H 276 MET cc_start: 0.7890 (tmm) cc_final: 0.7681 (tmm) REVERT: J 252 SER cc_start: 0.8494 (m) cc_final: 0.8160 (p) REVERT: K 284 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8628 (ttm170) REVERT: L 295 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7514 (m-80) outliers start: 31 outliers final: 21 residues processed: 126 average time/residue: 0.1331 time to fit residues: 20.9701 Evaluate side-chains 136 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 281 PHE Chi-restraints excluded: chain E residue 295 TYR 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 284 ARG 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 29 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.6305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3900 Z= 0.149 Angle : 0.487 3.496 5184 Z= 0.280 Chirality : 0.031 0.088 348 Planarity : 0.003 0.026 780 Dihedral : 3.920 12.595 588 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 8.33 % Allowed : 22.99 % 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: -3.45 (0.23), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (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 G 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 145 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.358 Fit side-chains REVERT: A 295 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: B 259 SER cc_start: 0.7854 (OUTLIER) cc_final: 0.7129 (p) REVERT: B 289 TYR cc_start: 0.8637 (m-80) cc_final: 0.7041 (p90) REVERT: C 263 PHE cc_start: 0.8727 (p90) cc_final: 0.8520 (p90) REVERT: C 276 MET cc_start: 0.8255 (tmm) cc_final: 0.7946 (tmm) REVERT: C 295 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7702 (m-80) REVERT: E 295 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: F 295 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7723 (m-80) REVERT: J 252 SER cc_start: 0.8491 (m) cc_final: 0.8159 (p) REVERT: K 280 ASN cc_start: 0.7269 (p0) cc_final: 0.6181 (t0) REVERT: K 284 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8829 (ttm-80) REVERT: L 280 ASN cc_start: 0.6969 (p0) cc_final: 0.6321 (t0) REVERT: L 295 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7552 (m-80) outliers start: 29 outliers final: 19 residues processed: 130 average time/residue: 0.1264 time to fit residues: 20.9121 Evaluate side-chains 137 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 281 PHE Chi-restraints excluded: chain E residue 295 TYR 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 284 ARG 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 33 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.6233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 3900 Z= 0.245 Angle : 0.532 3.866 5184 Z= 0.303 Chirality : 0.031 0.092 348 Planarity : 0.003 0.026 780 Dihedral : 4.284 12.694 588 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 8.91 % Allowed : 22.41 % 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: -3.50 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.003 PHE F 281 TYR 0.019 0.002 TYR J 266 ARG 0.002 0.000 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 143 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 0.386 Fit side-chains REVERT: A 295 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: C 295 TYR cc_start: 0.8210 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: E 295 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: F 295 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7827 (m-80) REVERT: J 252 SER cc_start: 0.8520 (m) cc_final: 0.8187 (p) REVERT: K 266 TYR cc_start: 0.8512 (m-80) cc_final: 0.8248 (m-80) REVERT: K 284 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8696 (ttm170) REVERT: L 280 ASN cc_start: 0.7614 (p0) cc_final: 0.6396 (t0) REVERT: L 295 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7559 (m-80) outliers start: 31 outliers final: 21 residues processed: 126 average time/residue: 0.1400 time to fit residues: 22.1959 Evaluate side-chains 136 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 E residue 252 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 295 TYR 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 271 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.6418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3900 Z= 0.151 Angle : 0.501 3.916 5184 Z= 0.286 Chirality : 0.031 0.095 348 Planarity : 0.003 0.024 780 Dihedral : 3.912 13.394 588 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 7.47 % Allowed : 24.14 % 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: -3.48 (0.23), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.032 0.002 PHE D 263 TYR 0.018 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 143 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 0.376 Fit side-chains REVERT: A 295 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7701 (m-80) REVERT: B 259 SER cc_start: 0.7583 (OUTLIER) cc_final: 0.6788 (p) REVERT: B 289 TYR cc_start: 0.8608 (m-80) cc_final: 0.7018 (p90) REVERT: C 295 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: E 295 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7925 (m-80) REVERT: G 252 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.8256 (p) REVERT: I 276 MET cc_start: 0.7758 (ttp) cc_final: 0.7530 (tmm) REVERT: J 252 SER cc_start: 0.8502 (m) cc_final: 0.8163 (p) REVERT: K 280 ASN cc_start: 0.6782 (p0) cc_final: 0.5892 (t0) REVERT: K 281 PHE cc_start: 0.5860 (m-80) cc_final: 0.4794 (p90) REVERT: K 284 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8841 (ttm-80) REVERT: L 280 ASN cc_start: 0.6941 (p0) cc_final: 0.6290 (t0) REVERT: L 295 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7502 (m-80) outliers start: 26 outliers final: 16 residues processed: 128 average time/residue: 0.1196 time to fit residues: 19.4709 Evaluate side-chains 136 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 E residue 252 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 295 TYR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4388 r_free = 0.4388 target = 0.143738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.130983 restraints weight = 7233.811| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 3.15 r_work: 0.4142 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.6429 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= 0.182 Angle : 0.518 4.037 5184 Z= 0.297 Chirality : 0.031 0.098 348 Planarity : 0.003 0.024 780 Dihedral : 3.962 13.686 588 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 7.18 % Allowed : 23.85 % 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: -3.51 (0.23), 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 0.022 0.002 PHE F 281 TYR 0.041 0.002 TYR E 266 ARG 0.003 0.001 ARG J 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1353.62 seconds wall clock time: 24 minutes 30.22 seconds (1470.22 seconds total)