Starting phenix.real_space_refine on Sun Mar 10 14:17:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/03_2024/7abk_11698.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/03_2024/7abk_11698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/03_2024/7abk_11698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/03_2024/7abk_11698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/03_2024/7abk_11698.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/03_2024/7abk_11698.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 2 5.16 5 C 977 2.51 5 N 289 2.21 5 O 306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 37": "OE1" <-> "OE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" 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: 1574 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1574 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 190} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 1.44, per 1000 atoms: 0.91 Number of scatterers: 1574 At special positions: 0 Unit cell: (69.6287, 180.364, 52.0118, 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 2 16.00 O 306 8.00 N 289 7.00 C 977 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: 0.73 Conformation dependent library (CDL) restraints added in 306.5 milliseconds 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 378 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 0 sheets defined 89.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 24 through 80 removed outlier: 3.593A pdb=" N LEU A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 155 removed outlier: 3.570A pdb=" N ALA A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ALA A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 186 removed outlier: 3.500A pdb=" N ASN A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 216 141 hydrogen bonds defined for protein. 423 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.40 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 558 1.34 - 1.46: 133 1.46 - 1.57: 895 1.57 - 1.69: 0 1.69 - 1.80: 4 Bond restraints: 1590 Sorted by residual: bond pdb=" N LYS A 151 " pdb=" CA LYS A 151 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.77e+00 bond pdb=" N ILE A 152 " pdb=" CA ILE A 152 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.29e-02 6.01e+03 7.12e+00 bond pdb=" N PHE A 54 " pdb=" CA PHE A 54 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 4.98e+00 bond pdb=" N GLU A 153 " pdb=" CA GLU A 153 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.30e-02 5.92e+03 4.81e+00 bond pdb=" CA THR A 53 " pdb=" C THR A 53 " ideal model delta sigma weight residual 1.523 1.542 -0.019 1.35e-02 5.49e+03 2.00e+00 ... (remaining 1585 not shown) Histogram of bond angle deviations from ideal: 100.63 - 107.29: 31 107.29 - 113.96: 919 113.96 - 120.62: 689 120.62 - 127.29: 487 127.29 - 133.95: 8 Bond angle restraints: 2134 Sorted by residual: angle pdb=" N GLU A 153 " pdb=" CA GLU A 153 " pdb=" C GLU A 153 " ideal model delta sigma weight residual 112.23 105.18 7.05 1.26e+00 6.30e-01 3.13e+01 angle pdb=" N PHE A 54 " pdb=" CA PHE A 54 " pdb=" C PHE A 54 " ideal model delta sigma weight residual 111.07 106.74 4.33 1.07e+00 8.73e-01 1.64e+01 angle pdb=" N ALA A 52 " pdb=" CA ALA A 52 " pdb=" C ALA A 52 " ideal model delta sigma weight residual 111.02 115.79 -4.77 1.22e+00 6.72e-01 1.53e+01 angle pdb=" N ILE A 152 " pdb=" CA ILE A 152 " pdb=" C ILE A 152 " ideal model delta sigma weight residual 112.80 109.11 3.69 1.15e+00 7.56e-01 1.03e+01 angle pdb=" C THR A 53 " pdb=" CA THR A 53 " pdb=" CB THR A 53 " ideal model delta sigma weight residual 110.67 105.27 5.40 1.92e+00 2.71e-01 7.91e+00 ... (remaining 2129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 891 17.40 - 34.80: 93 34.80 - 52.20: 17 52.20 - 69.60: 8 69.60 - 87.00: 4 Dihedral angle restraints: 1013 sinusoidal: 436 harmonic: 577 Sorted by residual: dihedral pdb=" CA ASP A 160 " pdb=" C ASP A 160 " pdb=" N ASN A 161 " pdb=" CA ASN A 161 " ideal model delta harmonic sigma weight residual 180.00 164.23 15.77 0 5.00e+00 4.00e-02 9.94e+00 dihedral pdb=" CA LYS A 151 " pdb=" CB LYS A 151 " pdb=" CG LYS A 151 " pdb=" CD LYS A 151 " ideal model delta sinusoidal sigma weight residual -180.00 -124.17 -55.83 3 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" CA LEU A 159 " pdb=" C LEU A 159 " pdb=" N ASP A 160 " pdb=" CA ASP A 160 " ideal model delta harmonic sigma weight residual 180.00 164.87 15.13 0 5.00e+00 4.00e-02 9.16e+00 ... (remaining 1010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 186 0.039 - 0.077: 39 0.077 - 0.116: 9 0.116 - 0.154: 1 0.154 - 0.192: 1 Chirality restraints: 236 Sorted by residual: chirality pdb=" CA ALA A 52 " pdb=" N ALA A 52 " pdb=" C ALA A 52 " pdb=" CB ALA A 52 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CA ILE A 152 " pdb=" N ILE A 152 " pdb=" C ILE A 152 " pdb=" CB ILE A 152 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA PHE A 54 " pdb=" N PHE A 54 " pdb=" C PHE A 54 " pdb=" CB PHE A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.33e-01 ... (remaining 233 not shown) Planarity restraints: 284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 150 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C GLN A 150 " 0.031 2.00e-02 2.50e+03 pdb=" O GLN A 150 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS A 151 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 188 " 0.016 5.00e-02 4.00e+02 2.41e-02 9.31e-01 pdb=" N PRO A 189 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 152 " -0.004 2.00e-02 2.50e+03 8.67e-03 7.52e-01 pdb=" C ILE A 152 " 0.015 2.00e-02 2.50e+03 pdb=" O ILE A 152 " -0.006 2.00e-02 2.50e+03 pdb=" N GLU A 153 " -0.005 2.00e-02 2.50e+03 ... (remaining 281 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 477 2.83 - 3.35: 1780 3.35 - 3.87: 2446 3.87 - 4.38: 2475 4.38 - 4.90: 4008 Nonbonded interactions: 11186 Sorted by model distance: nonbonded pdb=" OE2 GLU A 26 " pdb=" CD1 LEU A 143 " model vdw 2.315 3.460 nonbonded pdb=" O SER A 96 " pdb=" OG SER A 99 " model vdw 2.436 2.440 nonbonded pdb=" N GLU A 30 " pdb=" OE1 GLU A 30 " model vdw 2.443 2.520 nonbonded pdb=" OD1 ASN A 161 " pdb=" OG SER A 163 " model vdw 2.453 2.440 nonbonded pdb=" NH1 ARG A 44 " pdb=" OE2 GLU A 126 " model vdw 2.503 2.520 ... (remaining 11181 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 18.700 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.010 Find NCS groups from input model: 0.040 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.004 0.034 1590 Z= 0.281 Angle : 0.660 7.053 2134 Z= 0.437 Chirality : 0.037 0.192 236 Planarity : 0.003 0.024 284 Dihedral : 16.299 87.004 635 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.23 % Allowed : 6.17 % Favored : 92.59 % 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: 0.91 (0.56), residues: 194 helix: 0.77 (0.36), residues: 169 sheet: None (None), residues: 0 loop : 0.20 (1.53), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.012 0.003 PHE A 168 TYR 0.004 0.001 TYR A 129 ARG 0.002 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.199 Fit side-chains REVERT: A 45 ARG cc_start: 0.8815 (ttm110) cc_final: 0.8538 (ttm170) REVERT: A 58 GLU cc_start: 0.9103 (tt0) cc_final: 0.8547 (tm-30) REVERT: A 62 ASP cc_start: 0.9021 (m-30) cc_final: 0.6966 (m-30) REVERT: A 121 GLN cc_start: 0.8566 (mt0) cc_final: 0.8170 (tt0) REVERT: A 127 ARG cc_start: 0.8730 (ttm170) cc_final: 0.8493 (ttm-80) REVERT: A 128 LYS cc_start: 0.8914 (tptm) cc_final: 0.8441 (ttpt) REVERT: A 172 GLU cc_start: 0.8958 (tp30) cc_final: 0.8337 (tp30) REVERT: A 174 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8218 (ttpt) REVERT: A 177 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8642 (tm-30) REVERT: A 179 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8454 (tm-30) REVERT: A 195 LYS cc_start: 0.9568 (ttmt) cc_final: 0.8970 (tptp) REVERT: A 198 GLN cc_start: 0.9465 (tt0) cc_final: 0.9051 (tm-30) outliers start: 2 outliers final: 1 residues processed: 80 average time/residue: 0.2611 time to fit residues: 22.2100 Evaluate side-chains 55 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 0.0170 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1590 Z= 0.181 Angle : 0.543 4.896 2134 Z= 0.294 Chirality : 0.030 0.108 236 Planarity : 0.004 0.031 284 Dihedral : 5.715 53.643 220 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 4.32 % Allowed : 20.37 % Favored : 75.31 % 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: 3.83 (0.58), residues: 194 helix: 2.87 (0.37), residues: 171 sheet: None (None), residues: 0 loop : -0.32 (1.34), residues: 23 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.008 0.001 PHE A 168 TYR 0.009 0.001 TYR A 129 ARG 0.007 0.001 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.208 Fit side-chains REVERT: A 27 ASP cc_start: 0.9070 (t70) cc_final: 0.8832 (t0) REVERT: A 36 MET cc_start: 0.7666 (tpp) cc_final: 0.7253 (tpp) REVERT: A 58 GLU cc_start: 0.9133 (tt0) cc_final: 0.8691 (tm-30) REVERT: A 62 ASP cc_start: 0.9062 (m-30) cc_final: 0.7294 (m-30) REVERT: A 106 LYS cc_start: 0.8933 (mttt) cc_final: 0.8721 (mtmm) REVERT: A 123 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8158 (pp30) REVERT: A 128 LYS cc_start: 0.8832 (tptm) cc_final: 0.8399 (ttpt) REVERT: A 154 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8342 (tm-30) REVERT: A 174 LYS cc_start: 0.8534 (ttpt) cc_final: 0.8316 (ttmt) REVERT: A 177 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8723 (tm-30) REVERT: A 179 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8423 (tm-30) REVERT: A 195 LYS cc_start: 0.9580 (ttmt) cc_final: 0.9065 (tptt) REVERT: A 198 GLN cc_start: 0.9334 (tt0) cc_final: 0.9056 (tm-30) outliers start: 7 outliers final: 6 residues processed: 66 average time/residue: 0.2434 time to fit residues: 17.2057 Evaluate side-chains 64 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 193 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1590 Z= 0.158 Angle : 0.527 6.342 2134 Z= 0.264 Chirality : 0.029 0.111 236 Planarity : 0.003 0.023 284 Dihedral : 5.237 50.113 220 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.32 % Allowed : 21.60 % Favored : 74.07 % 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: 4.83 (0.59), residues: 194 helix: 3.59 (0.38), residues: 173 sheet: None (None), residues: 0 loop : -0.96 (1.15), residues: 21 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.006 0.001 PHE A 168 TYR 0.005 0.001 TYR A 129 ARG 0.006 0.001 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.220 Fit side-chains REVERT: A 36 MET cc_start: 0.7515 (tpp) cc_final: 0.7234 (tpp) REVERT: A 38 LEU cc_start: 0.9436 (mm) cc_final: 0.8998 (mm) REVERT: A 42 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8486 (mp0) REVERT: A 62 ASP cc_start: 0.9078 (m-30) cc_final: 0.8870 (m-30) REVERT: A 123 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8320 (pp30) REVERT: A 128 LYS cc_start: 0.8807 (tptm) cc_final: 0.8278 (ttpt) REVERT: A 154 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8393 (tm-30) REVERT: A 172 GLU cc_start: 0.8820 (tp30) cc_final: 0.8303 (tm-30) REVERT: A 177 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8740 (tm-30) REVERT: A 179 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8400 (tm-30) REVERT: A 195 LYS cc_start: 0.9581 (ttmt) cc_final: 0.9015 (tptt) REVERT: A 198 GLN cc_start: 0.9349 (tt0) cc_final: 0.9073 (tm-30) outliers start: 7 outliers final: 6 residues processed: 63 average time/residue: 0.2136 time to fit residues: 14.5990 Evaluate side-chains 64 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 193 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1590 Z= 0.162 Angle : 0.476 5.259 2134 Z= 0.249 Chirality : 0.030 0.113 236 Planarity : 0.003 0.023 284 Dihedral : 5.229 52.171 220 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 5.56 % Allowed : 23.46 % Favored : 70.99 % 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: 4.99 (0.57), residues: 194 helix: 3.69 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -0.70 (1.19), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.005 0.001 PHE A 168 TYR 0.003 0.001 TYR A 129 ARG 0.006 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.246 Fit side-chains REVERT: A 36 MET cc_start: 0.7518 (tpp) cc_final: 0.7255 (tpp) REVERT: A 55 LYS cc_start: 0.9522 (mmtp) cc_final: 0.8813 (pttt) REVERT: A 62 ASP cc_start: 0.9083 (m-30) cc_final: 0.8866 (m-30) REVERT: A 128 LYS cc_start: 0.8758 (tptm) cc_final: 0.8207 (ttpt) REVERT: A 154 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8381 (tm-30) REVERT: A 172 GLU cc_start: 0.8857 (tp30) cc_final: 0.8314 (tm-30) REVERT: A 177 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8758 (tm-30) REVERT: A 179 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8393 (tm-30) REVERT: A 195 LYS cc_start: 0.9574 (ttmt) cc_final: 0.9001 (tptt) REVERT: A 198 GLN cc_start: 0.9368 (tt0) cc_final: 0.9094 (tm-30) outliers start: 9 outliers final: 8 residues processed: 58 average time/residue: 0.2164 time to fit residues: 13.6181 Evaluate side-chains 62 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 193 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.0270 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 1590 Z= 0.153 Angle : 0.503 5.540 2134 Z= 0.255 Chirality : 0.030 0.113 236 Planarity : 0.003 0.032 284 Dihedral : 5.134 51.537 220 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.32 % Allowed : 26.54 % Favored : 69.14 % 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: 5.17 (0.58), residues: 194 helix: 3.84 (0.37), residues: 172 sheet: None (None), residues: 0 loop : -0.86 (1.20), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.005 0.001 PHE A 168 TYR 0.003 0.001 TYR A 129 ARG 0.005 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.196 Fit side-chains REVERT: A 36 MET cc_start: 0.7484 (tpp) cc_final: 0.7205 (tpp) REVERT: A 55 LYS cc_start: 0.9516 (mmtp) cc_final: 0.8796 (pttt) REVERT: A 62 ASP cc_start: 0.9076 (m-30) cc_final: 0.8842 (m-30) REVERT: A 128 LYS cc_start: 0.8682 (tptm) cc_final: 0.8055 (ttpt) REVERT: A 177 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8777 (tm-30) REVERT: A 179 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8369 (tm-30) REVERT: A 195 LYS cc_start: 0.9575 (ttmt) cc_final: 0.9008 (tptt) REVERT: A 198 GLN cc_start: 0.9373 (tt0) cc_final: 0.9099 (tm-30) outliers start: 7 outliers final: 6 residues processed: 58 average time/residue: 0.2147 time to fit residues: 13.5415 Evaluate side-chains 57 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 193 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1590 Z= 0.151 Angle : 0.516 5.515 2134 Z= 0.256 Chirality : 0.029 0.113 236 Planarity : 0.002 0.020 284 Dihedral : 5.128 52.642 220 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.32 % Allowed : 27.16 % Favored : 68.52 % 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: 5.29 (0.57), residues: 194 helix: 3.94 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -1.05 (1.18), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.004 0.001 PHE A 168 TYR 0.004 0.001 TYR A 129 ARG 0.007 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.202 Fit side-chains REVERT: A 55 LYS cc_start: 0.9515 (mmtp) cc_final: 0.8753 (pttt) REVERT: A 62 ASP cc_start: 0.9066 (m-30) cc_final: 0.8822 (m-30) REVERT: A 125 LEU cc_start: 0.8998 (mt) cc_final: 0.8791 (mp) REVERT: A 128 LYS cc_start: 0.8693 (tptm) cc_final: 0.8102 (ttpt) REVERT: A 133 LYS cc_start: 0.9419 (ttmm) cc_final: 0.8805 (ttmm) REVERT: A 177 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8775 (tm-30) REVERT: A 179 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8355 (tm-30) REVERT: A 195 LYS cc_start: 0.9573 (ttmt) cc_final: 0.8992 (tptt) REVERT: A 198 GLN cc_start: 0.9381 (tt0) cc_final: 0.9114 (tm-30) outliers start: 7 outliers final: 7 residues processed: 59 average time/residue: 0.2250 time to fit residues: 14.3328 Evaluate side-chains 59 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 193 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 14 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1590 Z= 0.208 Angle : 0.550 5.163 2134 Z= 0.279 Chirality : 0.031 0.113 236 Planarity : 0.003 0.025 284 Dihedral : 5.444 58.417 220 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.56 % Allowed : 24.07 % Favored : 70.37 % 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: 5.03 (0.57), residues: 194 helix: 3.74 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -0.84 (1.24), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 71 HIS 0.001 0.000 HIS A 100 PHE 0.004 0.001 PHE A 54 TYR 0.004 0.001 TYR A 129 ARG 0.007 0.001 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.154 Fit side-chains REVERT: A 37 GLU cc_start: 0.8839 (tp30) cc_final: 0.8411 (tp30) REVERT: A 55 LYS cc_start: 0.9532 (mmtp) cc_final: 0.8773 (pttt) REVERT: A 62 ASP cc_start: 0.9081 (m-30) cc_final: 0.8845 (m-30) REVERT: A 124 LYS cc_start: 0.9380 (mmmm) cc_final: 0.9118 (tppp) REVERT: A 128 LYS cc_start: 0.8759 (tptm) cc_final: 0.8144 (ttpt) REVERT: A 154 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8356 (tm-30) REVERT: A 177 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8751 (tm-30) REVERT: A 179 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8380 (tm-30) REVERT: A 195 LYS cc_start: 0.9586 (ttmt) cc_final: 0.9006 (tptt) REVERT: A 198 GLN cc_start: 0.9397 (tt0) cc_final: 0.9165 (tm-30) outliers start: 9 outliers final: 8 residues processed: 56 average time/residue: 0.1935 time to fit residues: 11.6958 Evaluate side-chains 61 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 193 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1590 Z= 0.174 Angle : 0.563 5.668 2134 Z= 0.276 Chirality : 0.030 0.114 236 Planarity : 0.003 0.025 284 Dihedral : 5.354 57.106 220 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.56 % Allowed : 25.31 % Favored : 69.14 % 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: 5.16 (0.57), residues: 194 helix: 3.83 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -0.85 (1.23), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.004 0.001 PHE A 168 TYR 0.004 0.001 TYR A 129 ARG 0.006 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.197 Fit side-chains REVERT: A 37 GLU cc_start: 0.8810 (tp30) cc_final: 0.8404 (tp30) REVERT: A 55 LYS cc_start: 0.9525 (mmtp) cc_final: 0.8761 (pttt) REVERT: A 62 ASP cc_start: 0.9069 (m-30) cc_final: 0.8823 (m-30) REVERT: A 124 LYS cc_start: 0.9368 (mmmm) cc_final: 0.9125 (tppp) REVERT: A 128 LYS cc_start: 0.8728 (tptm) cc_final: 0.8106 (ttpt) REVERT: A 133 LYS cc_start: 0.9417 (ttmm) cc_final: 0.8774 (ttmm) REVERT: A 154 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8267 (tm-30) REVERT: A 177 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8761 (tm-30) REVERT: A 179 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8372 (tm-30) REVERT: A 195 LYS cc_start: 0.9586 (ttmt) cc_final: 0.9012 (tptt) REVERT: A 198 GLN cc_start: 0.9390 (tt0) cc_final: 0.9164 (tm-30) outliers start: 9 outliers final: 8 residues processed: 53 average time/residue: 0.2261 time to fit residues: 12.9723 Evaluate side-chains 58 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 193 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1590 Z= 0.166 Angle : 0.559 5.892 2134 Z= 0.274 Chirality : 0.030 0.119 236 Planarity : 0.003 0.023 284 Dihedral : 5.225 54.746 220 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.94 % Allowed : 26.54 % Favored : 68.52 % 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: 5.21 (0.57), residues: 194 helix: 3.88 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -0.96 (1.19), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.004 0.001 PHE A 168 TYR 0.003 0.001 TYR A 129 ARG 0.007 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.199 Fit side-chains REVERT: A 55 LYS cc_start: 0.9522 (mmtp) cc_final: 0.8758 (pttt) REVERT: A 62 ASP cc_start: 0.9060 (m-30) cc_final: 0.8810 (m-30) REVERT: A 128 LYS cc_start: 0.8718 (tptm) cc_final: 0.8159 (ttpt) REVERT: A 133 LYS cc_start: 0.9421 (ttmm) cc_final: 0.8834 (ttmm) REVERT: A 172 GLU cc_start: 0.8868 (tp30) cc_final: 0.8340 (tm-30) REVERT: A 177 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8773 (tm-30) REVERT: A 179 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8374 (tm-30) REVERT: A 195 LYS cc_start: 0.9588 (ttmt) cc_final: 0.9016 (tptt) REVERT: A 198 GLN cc_start: 0.9390 (tt0) cc_final: 0.9164 (tm-30) outliers start: 8 outliers final: 8 residues processed: 57 average time/residue: 0.2246 time to fit residues: 13.8420 Evaluate side-chains 61 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 193 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1590 Z= 0.240 Angle : 0.612 5.587 2134 Z= 0.311 Chirality : 0.033 0.133 236 Planarity : 0.003 0.023 284 Dihedral : 4.834 41.071 220 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 5.56 % Allowed : 25.93 % Favored : 68.52 % 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: 4.79 (0.56), residues: 194 helix: 3.56 (0.35), residues: 172 sheet: None (None), residues: 0 loop : -0.75 (1.20), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 71 HIS 0.001 0.001 HIS A 100 PHE 0.004 0.001 PHE A 168 TYR 0.004 0.001 TYR A 129 ARG 0.007 0.001 ARG A 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 388 Ramachandran restraints generated. 194 Oldfield, 0 Emsley, 194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.185 Fit side-chains REVERT: A 37 GLU cc_start: 0.8878 (tp30) cc_final: 0.8469 (tp30) REVERT: A 55 LYS cc_start: 0.9535 (mmtp) cc_final: 0.8765 (pttt) REVERT: A 62 ASP cc_start: 0.9092 (m-30) cc_final: 0.8846 (m-30) REVERT: A 128 LYS cc_start: 0.8822 (tptm) cc_final: 0.8241 (ttpt) REVERT: A 154 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8309 (tm-30) REVERT: A 177 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8729 (tm-30) REVERT: A 179 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8408 (tm-30) REVERT: A 195 LYS cc_start: 0.9591 (ttmt) cc_final: 0.9059 (tptt) REVERT: A 198 GLN cc_start: 0.9386 (tt0) cc_final: 0.9173 (tm-30) outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 0.2380 time to fit residues: 14.5682 Evaluate side-chains 60 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 193 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** 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 = 0.3821 r_free = 0.3821 target = 0.105630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.085349 restraints weight = 3805.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.087777 restraints weight = 1791.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.089331 restraints weight = 1128.703| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1590 Z= 0.175 Angle : 0.588 5.885 2134 Z= 0.294 Chirality : 0.030 0.127 236 Planarity : 0.002 0.020 284 Dihedral : 3.355 11.261 216 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.70 % Allowed : 29.01 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.11 (0.57), residues: 194 helix: 3.80 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -0.89 (1.19), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.005 0.001 PHE A 168 TYR 0.004 0.001 TYR A 129 ARG 0.005 0.000 ARG A 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 998.90 seconds wall clock time: 19 minutes 57.13 seconds (1197.13 seconds total)