Starting phenix.real_space_refine on Sun Mar 10 18:00:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/03_2024/7zj2_14739.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/03_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_14739/03_2024/7zj2_14739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/03_2024/7zj2_14739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/03_2024/7zj2_14739.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj2_14739/03_2024/7zj2_14739.pdb" } 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 Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3792 Number of models: 1 Model: "" Number of chains: 12 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} Chain: "B" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "C" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "D" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "E" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "F" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "G" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "H" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "I" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "J" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "K" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "L" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Time building chain proxies: 2.11, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 1.41 Conformation dependent library (CDL) restraints added in 667.3 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: 0.29 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: 0.06 Time building geometry restraints manager: 1.55 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: 100.21 - 105.51: 180 105.51 - 110.81: 555 110.81 - 116.11: 1034 116.11 - 121.41: 2124 121.41 - 126.72: 1291 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 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: 0.730 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: 3.520 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.540 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.700 ------------------------------------------------------------------------------- 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 : 0.373 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: 0.1587 time to fit residues: 46.1324 Evaluate side-chains 180 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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: 0.8980 chunk 36 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** 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: 0.7726 moved from start: 0.4353 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= 0.139 Angle : 0.544 4.301 5184 Z= 0.310 Chirality : 0.029 0.075 348 Planarity : 0.003 0.022 780 Dihedral : 4.400 10.943 588 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.03 % Allowed : 23.28 % 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: -3.69 (0.25), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.19), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.002 PHE C 263 TYR 0.020 0.002 TYR G 260 ARG 0.002 0.001 ARG J 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 178 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 157 time to evaluate : 0.358 Fit side-chains REVERT: A 263 PHE cc_start: 0.8460 (p90) cc_final: 0.7035 (m-80) REVERT: A 284 ARG cc_start: 0.8681 (ttt180) cc_final: 0.5752 (mtt90) REVERT: A 289 TYR cc_start: 0.8728 (m-80) cc_final: 0.7065 (p90) REVERT: B 263 PHE cc_start: 0.8607 (p90) cc_final: 0.7085 (m-80) REVERT: B 289 TYR cc_start: 0.8543 (m-80) cc_final: 0.6944 (p90) REVERT: C 252 SER cc_start: 0.8536 (m) cc_final: 0.8236 (m) REVERT: C 263 PHE cc_start: 0.8507 (p90) cc_final: 0.8246 (p90) REVERT: D 263 PHE cc_start: 0.8559 (p90) cc_final: 0.8355 (p90) REVERT: I 263 PHE cc_start: 0.8579 (p90) cc_final: 0.8337 (p90) REVERT: I 272 ASN cc_start: 0.7824 (t0) cc_final: 0.7396 (t0) REVERT: I 276 MET cc_start: 0.7648 (ttp) cc_final: 0.7337 (ttp) REVERT: J 252 SER cc_start: 0.8332 (m) cc_final: 0.7887 (m) REVERT: J 259 SER cc_start: 0.8931 (m) cc_final: 0.8558 (p) REVERT: J 276 MET cc_start: 0.7850 (ttp) cc_final: 0.5810 (ttp) REVERT: K 280 ASN cc_start: 0.8034 (p0) cc_final: 0.7369 (t0) REVERT: L 280 ASN cc_start: 0.8174 (p0) cc_final: 0.7041 (m-40) REVERT: L 281 PHE cc_start: 0.7526 (m-80) cc_final: 0.7178 (m-80) outliers start: 21 outliers final: 15 residues processed: 165 average time/residue: 0.1283 time to fit residues: 26.8104 Evaluate side-chains 160 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 252 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 270 SER Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 270 SER Chi-restraints excluded: chain 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: 6.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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** ** H 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 ASN ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 3900 Z= 0.255 Angle : 0.554 5.455 5184 Z= 0.318 Chirality : 0.031 0.104 348 Planarity : 0.004 0.022 780 Dihedral : 4.704 10.968 588 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 9.20 % Allowed : 21.55 % 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: -3.65 (0.23), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.034 0.003 PHE F 263 TYR 0.019 0.002 TYR H 266 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 166 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 0.453 Fit side-chains REVERT: A 289 TYR cc_start: 0.8740 (m-80) cc_final: 0.7045 (p90) REVERT: A 295 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7586 (m-80) REVERT: B 259 SER cc_start: 0.7800 (OUTLIER) cc_final: 0.7078 (p) REVERT: C 252 SER cc_start: 0.8409 (m) cc_final: 0.8104 (m) REVERT: C 261 ASN cc_start: 0.8780 (m-40) cc_final: 0.8528 (m-40) REVERT: C 263 PHE cc_start: 0.8670 (p90) cc_final: 0.8376 (p90) REVERT: D 263 PHE cc_start: 0.8683 (p90) cc_final: 0.8479 (p90) REVERT: F 259 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8403 (p) REVERT: F 295 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.7122 (m-80) REVERT: J 259 SER cc_start: 0.9006 (m) cc_final: 0.8717 (p) REVERT: J 261 ASN cc_start: 0.8800 (m-40) cc_final: 0.8491 (m-40) REVERT: K 272 ASN cc_start: 0.8430 (p0) cc_final: 0.7572 (t0) outliers start: 32 outliers final: 24 residues processed: 149 average time/residue: 0.1318 time to fit residues: 24.9240 Evaluate side-chains 159 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 259 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 259 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 261 ASN 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: 4.9990 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7853 moved from start: 0.5460 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= 0.178 Angle : 0.494 3.311 5184 Z= 0.282 Chirality : 0.030 0.085 348 Planarity : 0.003 0.015 780 Dihedral : 4.095 9.680 588 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.91 % Allowed : 23.28 % 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: -3.55 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.029 0.003 PHE G 281 TYR 0.019 0.002 TYR J 266 ARG 0.003 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 165 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 0.426 Fit side-chains REVERT: A 289 TYR cc_start: 0.8745 (m-80) cc_final: 0.7060 (p90) REVERT: A 295 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: B 259 SER cc_start: 0.7739 (OUTLIER) cc_final: 0.7075 (p) REVERT: B 289 TYR cc_start: 0.8606 (m-80) cc_final: 0.7092 (p90) REVERT: C 263 PHE cc_start: 0.8653 (p90) cc_final: 0.8398 (p90) REVERT: E 262 ASP cc_start: 0.7758 (t0) cc_final: 0.7536 (t0) REVERT: F 295 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7010 (m-80) REVERT: J 261 ASN cc_start: 0.8714 (m-40) cc_final: 0.8426 (m-40) REVERT: K 272 ASN cc_start: 0.8515 (p0) cc_final: 0.8219 (p0) outliers start: 31 outliers final: 24 residues processed: 149 average time/residue: 0.1274 time to fit residues: 24.1669 Evaluate side-chains 153 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 261 ASN Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 295 TYR Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 270 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.0170 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 ASN ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7769 moved from start: 0.5772 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= 0.120 Angle : 0.458 3.166 5184 Z= 0.261 Chirality : 0.029 0.079 348 Planarity : 0.003 0.013 780 Dihedral : 3.638 9.313 588 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 10.06 % Allowed : 21.26 % 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: -3.44 (0.23), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.002 PHE F 281 TYR 0.018 0.002 TYR D 260 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 163 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 0.415 Fit side-chains REVERT: A 259 SER cc_start: 0.7985 (OUTLIER) cc_final: 0.7463 (p) REVERT: A 289 TYR cc_start: 0.8731 (m-80) cc_final: 0.7073 (p90) REVERT: A 295 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7570 (m-80) REVERT: B 289 TYR cc_start: 0.8564 (m-80) cc_final: 0.7074 (p90) REVERT: C 263 PHE cc_start: 0.8676 (p90) cc_final: 0.8416 (p90) REVERT: C 295 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.7559 (m-80) REVERT: D 263 PHE cc_start: 0.8443 (p90) cc_final: 0.8243 (p90) REVERT: F 295 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7082 (m-80) REVERT: K 280 ASN cc_start: 0.7409 (p0) cc_final: 0.6538 (t0) REVERT: L 295 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7377 (m-80) outliers start: 35 outliers final: 26 residues processed: 146 average time/residue: 0.1216 time to fit residues: 22.6793 Evaluate side-chains 149 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 259 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 252 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 261 ASN Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 295 TYR Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 270 SER Chi-restraints excluded: chain L residue 295 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 24 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 261 ASN ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3900 Z= 0.198 Angle : 0.492 4.388 5184 Z= 0.280 Chirality : 0.029 0.079 348 Planarity : 0.003 0.018 780 Dihedral : 3.869 10.676 588 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 11.21 % Allowed : 20.69 % 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: -3.42 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (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 J 266 ARG 0.002 0.001 ARG J 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 120 time to evaluate : 0.442 Fit side-chains REVERT: A 259 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7484 (p) REVERT: A 295 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: C 263 PHE cc_start: 0.8765 (p90) cc_final: 0.8520 (p90) REVERT: C 295 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: E 295 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: F 295 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7138 (m-80) REVERT: L 295 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7433 (m-80) outliers start: 39 outliers final: 27 residues processed: 141 average time/residue: 0.1197 time to fit residues: 21.6550 Evaluate side-chains 150 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 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 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 259 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 259 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 252 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 261 ASN Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 270 SER Chi-restraints excluded: chain L residue 276 MET 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: 3.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 3900 Z= 0.269 Angle : 0.529 3.590 5184 Z= 0.299 Chirality : 0.030 0.086 348 Planarity : 0.003 0.021 780 Dihedral : 4.144 10.965 588 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 10.63 % Allowed : 21.26 % 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: -3.43 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.028 0.003 PHE F 281 TYR 0.021 0.002 TYR J 266 ARG 0.002 0.000 ARG J 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 117 time to evaluate : 0.422 Fit side-chains REVERT: A 259 SER cc_start: 0.8051 (OUTLIER) cc_final: 0.7480 (p) REVERT: A 295 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: C 276 MET cc_start: 0.8344 (tmm) cc_final: 0.7989 (tmm) REVERT: C 295 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: E 295 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7969 (m-80) REVERT: F 295 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: H 266 TYR cc_start: 0.8803 (m-80) cc_final: 0.8494 (m-80) REVERT: H 295 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: L 295 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7538 (m-80) outliers start: 37 outliers final: 25 residues processed: 138 average time/residue: 0.1250 time to fit residues: 22.0304 Evaluate side-chains 144 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 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 259 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 G residue 285 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 295 TYR Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 295 TYR Chi-restraints excluded: chain J 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 261 ASN Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 270 SER Chi-restraints excluded: chain L residue 276 MET 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: 3.9990 chunk 31 optimal weight: 0.0050 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 43 optimal weight: 0.0060 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.1814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.6242 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= 0.174 Angle : 0.486 3.647 5184 Z= 0.274 Chirality : 0.030 0.091 348 Planarity : 0.003 0.020 780 Dihedral : 3.787 11.075 588 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 9.48 % Allowed : 23.28 % Favored : 67.24 % 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: -3.40 (0.23), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.002 PHE F 281 TYR 0.020 0.002 TYR J 266 ARG 0.003 0.000 ARG E 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 154 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 0.418 Fit side-chains REVERT: A 259 SER cc_start: 0.7933 (OUTLIER) cc_final: 0.7290 (p) REVERT: A 295 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: B 259 SER cc_start: 0.7802 (OUTLIER) cc_final: 0.7154 (p) REVERT: B 289 TYR cc_start: 0.8624 (m-80) cc_final: 0.6987 (p90) REVERT: C 276 MET cc_start: 0.8289 (tmm) cc_final: 0.7968 (tmm) REVERT: C 295 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: D 263 PHE cc_start: 0.8554 (p90) cc_final: 0.8242 (p90) REVERT: E 295 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7920 (m-80) REVERT: F 295 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7690 (m-80) REVERT: H 266 TYR cc_start: 0.8873 (m-80) cc_final: 0.8664 (m-80) REVERT: H 295 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: K 281 PHE cc_start: 0.6188 (m-80) cc_final: 0.5957 (m-80) REVERT: L 295 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7583 (m-80) outliers start: 33 outliers final: 25 residues processed: 138 average time/residue: 0.1251 time to fit residues: 22.1800 Evaluate side-chains 148 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 259 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 G residue 259 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 295 TYR Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J 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 261 ASN Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 295 TYR Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 276 MET 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: 2.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.6212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.037 3900 Z= 0.367 Angle : 0.583 4.755 5184 Z= 0.328 Chirality : 0.032 0.100 348 Planarity : 0.003 0.023 780 Dihedral : 4.513 12.670 588 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 10.06 % Allowed : 22.99 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (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 0.031 0.003 PHE F 281 TYR 0.023 0.002 TYR J 266 ARG 0.002 0.001 ARG F 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 136 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 101 time to evaluate : 0.415 Fit side-chains REVERT: A 295 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: C 276 MET cc_start: 0.8286 (tmm) cc_final: 0.7956 (tmm) REVERT: C 295 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: F 295 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: H 295 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: L 281 PHE cc_start: 0.6431 (m-80) cc_final: 0.5067 (p90) REVERT: L 295 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7658 (m-80) outliers start: 35 outliers final: 26 residues processed: 121 average time/residue: 0.1330 time to fit residues: 20.3490 Evaluate side-chains 133 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 102 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 259 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER 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 285 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 295 TYR Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J 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 261 ASN Chi-restraints excluded: chain K residue 265 ASN Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 270 SER Chi-restraints excluded: chain L residue 276 MET 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: 3.9990 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 0.0020 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 261 ASN ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.6445 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= 0.119 Angle : 0.478 3.911 5184 Z= 0.271 Chirality : 0.032 0.096 348 Planarity : 0.003 0.019 780 Dihedral : 3.620 11.283 588 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 7.76 % Allowed : 25.86 % 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: -3.41 (0.23), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.028 0.002 PHE H 263 TYR 0.030 0.002 TYR H 266 ARG 0.002 0.001 ARG E 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 149 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 0.424 Fit side-chains REVERT: A 259 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.7575 (p) REVERT: A 289 TYR cc_start: 0.8723 (m-80) cc_final: 0.6897 (p90) REVERT: A 295 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: B 259 SER cc_start: 0.7831 (OUTLIER) cc_final: 0.7176 (p) REVERT: B 289 TYR cc_start: 0.8626 (m-80) cc_final: 0.6998 (p90) REVERT: C 295 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7707 (m-80) REVERT: H 295 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: K 280 ASN cc_start: 0.6857 (p0) cc_final: 0.6089 (t0) REVERT: K 281 PHE cc_start: 0.5929 (m-80) cc_final: 0.4969 (p90) REVERT: L 280 ASN cc_start: 0.6719 (p0) cc_final: 0.5934 (t0) REVERT: L 281 PHE cc_start: 0.5922 (m-80) cc_final: 0.4826 (p90) REVERT: L 295 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7518 (m-80) outliers start: 27 outliers final: 20 residues processed: 134 average time/residue: 0.1286 time to fit residues: 22.0328 Evaluate side-chains 143 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 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 259 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER 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 H residue 295 TYR Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 270 SER Chi-restraints excluded: chain J 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 Chi-restraints excluded: chain L residue 276 MET 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: 4.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 0.0470 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.129334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.117262 restraints weight = 7193.204| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.91 r_work: 0.3980 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.6333 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= 0.320 Angle : 0.568 3.991 5184 Z= 0.323 Chirality : 0.032 0.091 348 Planarity : 0.003 0.023 780 Dihedral : 4.351 11.832 588 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 8.91 % Allowed : 24.14 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.003 PHE F 281 TYR 0.032 0.002 TYR F 266 ARG 0.002 0.001 ARG J 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1370.74 seconds wall clock time: 25 minutes 12.32 seconds (1512.32 seconds total)