Starting phenix.real_space_refine on Mon Sep 23 11:32:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/09_2024/7abk_11698.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/09_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_11698/09_2024/7abk_11698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/09_2024/7abk_11698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/09_2024/7abk_11698.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abk_11698/09_2024/7abk_11698.cif" } 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. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 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: 4.02, per 1000 atoms: 2.55 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 193.0 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: 0.12 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: 0.50 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: 0.00 - 1.41: 2037 1.41 - 2.82: 77 2.82 - 4.23: 16 4.23 - 5.64: 3 5.64 - 7.05: 1 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 3.040 nonbonded pdb=" N GLU A 30 " pdb=" OE1 GLU A 30 " model vdw 2.443 3.120 nonbonded pdb=" OD1 ASN A 161 " pdb=" OG SER A 163 " model vdw 2.453 3.040 nonbonded pdb=" NH1 ARG A 44 " pdb=" OE2 GLU A 126 " model vdw 2.503 3.120 ... (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: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.950 Find NCS groups from input model: 0.010 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.600 ------------------------------------------------------------------------------- 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 : 0.209 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: 0.2437 time to fit residues: 20.7689 Evaluate side-chains 55 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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: 9.9990 chunk 14 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1590 Z= 0.194 Angle : 0.564 5.263 2134 Z= 0.303 Chirality : 0.030 0.104 236 Planarity : 0.004 0.028 284 Dihedral : 5.853 55.007 220 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.09 % Allowed : 18.52 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.58), residues: 194 helix: 2.75 (0.37), residues: 172 sheet: None (None), residues: 0 loop : -0.99 (1.23), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.008 0.002 PHE A 168 TYR 0.009 0.002 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 72 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.202 Fit side-chains REVERT: A 36 MET cc_start: 0.7722 (tpp) cc_final: 0.7347 (tpp) REVERT: A 58 GLU cc_start: 0.9132 (tt0) cc_final: 0.8628 (tm-30) REVERT: A 62 ASP cc_start: 0.9058 (m-30) cc_final: 0.7283 (m-30) REVERT: A 121 GLN cc_start: 0.8547 (mt0) cc_final: 0.8253 (tt0) REVERT: A 123 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8082 (pp30) REVERT: A 128 LYS cc_start: 0.8834 (tptm) cc_final: 0.8409 (ttpt) REVERT: A 174 LYS cc_start: 0.8542 (ttpt) cc_final: 0.8312 (ttmt) REVERT: A 177 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8750 (tm-30) REVERT: A 179 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8422 (tm-30) REVERT: A 195 LYS cc_start: 0.9581 (ttmt) cc_final: 0.9064 (tptt) REVERT: A 198 GLN cc_start: 0.9345 (tt0) cc_final: 0.9077 (tm-30) REVERT: A 212 MET cc_start: 0.8076 (tpt) cc_final: 0.7138 (tpt) outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 0.2466 time to fit residues: 18.2205 Evaluate side-chains 61 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 151 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8427 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1590 Z= 0.181 Angle : 0.579 6.631 2134 Z= 0.292 Chirality : 0.030 0.110 236 Planarity : 0.003 0.024 284 Dihedral : 5.377 50.346 220 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.47 % Allowed : 20.99 % Favored : 76.54 % 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: 4.41 (0.57), residues: 194 helix: 3.31 (0.37), residues: 173 sheet: None (None), residues: 0 loop : -1.10 (1.13), residues: 21 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 71 HIS 0.001 0.000 HIS A 100 PHE 0.006 0.001 PHE A 168 TYR 0.010 0.001 TYR A 129 ARG 0.005 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 65 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.216 Fit side-chains REVERT: A 36 MET cc_start: 0.7576 (tpp) cc_final: 0.7275 (tpp) REVERT: A 62 ASP cc_start: 0.9083 (m-30) cc_final: 0.8878 (m-30) REVERT: A 121 GLN cc_start: 0.8541 (mt0) cc_final: 0.8190 (tt0) REVERT: A 123 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8188 (pp30) REVERT: A 128 LYS cc_start: 0.8784 (tptm) cc_final: 0.8328 (ttpt) REVERT: A 154 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8437 (tm-30) REVERT: A 177 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8752 (tm-30) REVERT: A 179 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8412 (tm-30) REVERT: A 195 LYS cc_start: 0.9580 (ttmt) cc_final: 0.9013 (tptt) REVERT: A 198 GLN cc_start: 0.9353 (tt0) cc_final: 0.9072 (tm-30) REVERT: A 200 GLU cc_start: 0.9147 (pp20) cc_final: 0.8858 (pp20) outliers start: 4 outliers final: 4 residues processed: 63 average time/residue: 0.2303 time to fit residues: 15.6500 Evaluate side-chains 63 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 8.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1590 Z= 0.174 Angle : 0.521 5.138 2134 Z= 0.267 Chirality : 0.031 0.113 236 Planarity : 0.003 0.022 284 Dihedral : 5.317 52.241 220 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.32 % Allowed : 22.84 % Favored : 72.84 % 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: 5.01 (0.58), residues: 194 helix: 3.71 (0.37), residues: 172 sheet: None (None), residues: 0 loop : -0.72 (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 0.005 0.001 PHE A 168 TYR 0.010 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 71 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.191 Fit side-chains REVERT: A 36 MET cc_start: 0.7572 (tpp) cc_final: 0.7262 (tpp) REVERT: A 62 ASP cc_start: 0.9093 (m-30) cc_final: 0.8876 (m-30) REVERT: A 121 GLN cc_start: 0.8574 (mt0) cc_final: 0.8189 (tt0) REVERT: A 128 LYS cc_start: 0.8796 (tptm) cc_final: 0.8255 (ttpt) REVERT: A 154 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8347 (tm-30) REVERT: A 172 GLU cc_start: 0.8878 (tp30) cc_final: 0.8301 (tm-30) REVERT: A 177 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8743 (tm-30) REVERT: A 179 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8401 (tm-30) REVERT: A 195 LYS cc_start: 0.9576 (ttmt) cc_final: 0.9010 (tptt) REVERT: A 198 GLN cc_start: 0.9369 (tt0) cc_final: 0.9092 (tm-30) REVERT: A 200 GLU cc_start: 0.9164 (pp20) cc_final: 0.8862 (pp20) outliers start: 7 outliers final: 6 residues processed: 66 average time/residue: 0.2039 time to fit residues: 14.5490 Evaluate side-chains 63 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1590 Z= 0.168 Angle : 0.559 7.300 2134 Z= 0.275 Chirality : 0.032 0.112 236 Planarity : 0.003 0.022 284 Dihedral : 5.256 52.425 220 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 6.17 % Allowed : 22.22 % Favored : 71.60 % 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: 5.10 (0.57), residues: 194 helix: 3.78 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -0.81 (1.21), 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 0.009 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 69 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.195 Fit side-chains REVERT: A 36 MET cc_start: 0.7477 (tpp) cc_final: 0.7183 (tpp) REVERT: A 55 LYS cc_start: 0.9520 (mmtp) cc_final: 0.8809 (pttt) REVERT: A 62 ASP cc_start: 0.9092 (m-30) cc_final: 0.8870 (m-30) REVERT: A 121 GLN cc_start: 0.8457 (mt0) cc_final: 0.8210 (tt0) REVERT: A 124 LYS cc_start: 0.9286 (ttmm) cc_final: 0.8998 (tppp) REVERT: A 128 LYS cc_start: 0.8748 (tptm) cc_final: 0.8177 (ttpt) REVERT: A 154 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8294 (tm-30) REVERT: A 177 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8741 (tm-30) REVERT: A 179 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8385 (tm-30) REVERT: A 195 LYS cc_start: 0.9578 (ttmt) cc_final: 0.8995 (tptt) REVERT: A 198 GLN cc_start: 0.9377 (tt0) cc_final: 0.9109 (tm-30) REVERT: A 200 GLU cc_start: 0.9183 (pp20) cc_final: 0.8858 (pp20) outliers start: 10 outliers final: 8 residues processed: 63 average time/residue: 0.2127 time to fit residues: 14.5339 Evaluate side-chains 66 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1590 Z= 0.166 Angle : 0.605 12.541 2134 Z= 0.285 Chirality : 0.031 0.113 236 Planarity : 0.003 0.024 284 Dihedral : 5.195 53.063 220 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.94 % Allowed : 24.07 % 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: 5.20 (0.57), residues: 194 helix: 3.87 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -0.99 (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 0.008 0.001 TYR A 129 ARG 0.006 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 67 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.191 Fit side-chains REVERT: A 27 ASP cc_start: 0.9038 (t0) cc_final: 0.8774 (t0) REVERT: A 55 LYS cc_start: 0.9515 (mmtp) cc_final: 0.8795 (pttt) REVERT: A 62 ASP cc_start: 0.9073 (m-30) cc_final: 0.8837 (m-30) REVERT: A 124 LYS cc_start: 0.9246 (ttmm) cc_final: 0.9039 (tppp) REVERT: A 128 LYS cc_start: 0.8734 (tptm) cc_final: 0.8146 (ttpt) REVERT: A 177 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8751 (tm-30) REVERT: A 179 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8371 (tm-30) REVERT: A 195 LYS cc_start: 0.9578 (ttmt) cc_final: 0.8995 (tptt) REVERT: A 198 GLN cc_start: 0.9386 (tt0) cc_final: 0.9117 (tm-30) REVERT: A 200 GLU cc_start: 0.9212 (pp20) cc_final: 0.8888 (pp20) outliers start: 8 outliers final: 5 residues processed: 63 average time/residue: 0.2078 time to fit residues: 14.1620 Evaluate side-chains 65 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 100 HIS Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 152 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1590 Z= 0.163 Angle : 0.584 6.655 2134 Z= 0.280 Chirality : 0.032 0.136 236 Planarity : 0.002 0.020 284 Dihedral : 5.205 54.219 220 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.46 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: 5.33 (0.57), residues: 194 helix: 3.95 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -0.92 (1.21), 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 0.004 0.001 PHE A 168 TYR 0.009 0.001 TYR A 129 ARG 0.006 0.000 ARG A 127 *********************** 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 79 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 55 LYS cc_start: 0.9510 (mmtp) cc_final: 0.8732 (pttt) REVERT: A 58 GLU cc_start: 0.9070 (tt0) cc_final: 0.8631 (tp30) REVERT: A 62 ASP cc_start: 0.9071 (m-30) cc_final: 0.7955 (m-30) REVERT: A 128 LYS cc_start: 0.8704 (tptm) cc_final: 0.8074 (ttpt) REVERT: A 150 GLN cc_start: 0.9213 (tt0) cc_final: 0.8828 (tm-30) REVERT: A 177 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8756 (tm-30) REVERT: A 179 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8360 (tm-30) REVERT: A 195 LYS cc_start: 0.9578 (ttmt) cc_final: 0.8997 (tptt) REVERT: A 197 GLU cc_start: 0.9307 (pp20) cc_final: 0.9015 (pp20) REVERT: A 198 GLN cc_start: 0.9396 (tt0) cc_final: 0.8991 (tm-30) REVERT: A 200 GLU cc_start: 0.9219 (pp20) cc_final: 0.8917 (pp20) REVERT: A 201 GLU cc_start: 0.9223 (pp20) cc_final: 0.9003 (pp20) outliers start: 9 outliers final: 9 residues processed: 73 average time/residue: 0.2081 time to fit residues: 16.3979 Evaluate side-chains 64 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU 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 132 LEU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 152 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1590 Z= 0.178 Angle : 0.645 6.430 2134 Z= 0.306 Chirality : 0.031 0.113 236 Planarity : 0.003 0.029 284 Dihedral : 5.191 53.218 220 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.32 % Allowed : 25.93 % Favored : 69.75 % 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: 5.31 (0.57), residues: 194 helix: 3.95 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -1.01 (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 0.004 0.001 PHE A 168 TYR 0.009 0.001 TYR A 129 ARG 0.007 0.001 ARG A 59 *********************** 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 62 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9137 (tp30) cc_final: 0.8867 (mm-30) REVERT: A 55 LYS cc_start: 0.9502 (mmtp) cc_final: 0.8737 (pttt) REVERT: A 62 ASP cc_start: 0.9060 (m-30) cc_final: 0.8818 (m-30) REVERT: A 128 LYS cc_start: 0.8675 (tptm) cc_final: 0.8005 (ttpt) REVERT: A 150 GLN cc_start: 0.9178 (tt0) cc_final: 0.8805 (tm-30) REVERT: A 177 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8775 (tm-30) REVERT: A 179 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8335 (tm-30) REVERT: A 195 LYS cc_start: 0.9578 (ttmt) cc_final: 0.8992 (tptt) REVERT: A 198 GLN cc_start: 0.9377 (tt0) cc_final: 0.9134 (tm-30) REVERT: A 200 GLU cc_start: 0.9215 (pp20) cc_final: 0.8883 (pp20) outliers start: 7 outliers final: 6 residues processed: 59 average time/residue: 0.2254 time to fit residues: 14.3467 Evaluate side-chains 63 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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: 0.8405 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1590 Z= 0.205 Angle : 0.664 6.358 2134 Z= 0.318 Chirality : 0.031 0.113 236 Planarity : 0.003 0.031 284 Dihedral : 5.482 59.062 220 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.56 % Allowed : 24.69 % Favored : 69.75 % 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: 5.13 (0.57), residues: 194 helix: 3.82 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -0.97 (1.20), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.004 0.001 PHE A 168 TYR 0.009 0.001 TYR A 129 ARG 0.006 0.001 ARG A 59 *********************** 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 65 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9158 (tp30) cc_final: 0.8871 (mm-30) REVERT: A 55 LYS cc_start: 0.9517 (mmtp) cc_final: 0.8759 (pttt) REVERT: A 62 ASP cc_start: 0.9067 (m-30) cc_final: 0.8824 (m-30) REVERT: A 128 LYS cc_start: 0.8700 (tptm) cc_final: 0.8083 (ttpt) REVERT: A 133 LYS cc_start: 0.9456 (ttmm) cc_final: 0.9075 (ttmm) REVERT: A 177 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8738 (tm-30) REVERT: A 179 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8374 (tm-30) REVERT: A 195 LYS cc_start: 0.9583 (ttmt) cc_final: 0.8998 (tptt) REVERT: A 198 GLN cc_start: 0.9399 (tt0) cc_final: 0.9188 (tm-30) outliers start: 9 outliers final: 8 residues processed: 60 average time/residue: 0.2214 time to fit residues: 14.3674 Evaluate side-chains 63 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 53 THR 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 132 LEU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 152 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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: 0.8416 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1590 Z= 0.211 Angle : 0.663 6.510 2134 Z= 0.322 Chirality : 0.032 0.115 236 Planarity : 0.003 0.028 284 Dihedral : 5.382 55.844 220 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.94 % Allowed : 27.16 % Favored : 67.90 % 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: 4.96 (0.56), residues: 194 helix: 3.70 (0.35), residues: 172 sheet: None (None), residues: 0 loop : -0.96 (1.21), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.004 0.001 PHE A 168 TYR 0.010 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 66 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 55 LYS cc_start: 0.9513 (mmtp) cc_final: 0.8754 (pttt) REVERT: A 62 ASP cc_start: 0.9080 (m-30) cc_final: 0.8832 (m-30) REVERT: A 128 LYS cc_start: 0.8767 (tptm) cc_final: 0.8149 (ttpt) REVERT: A 177 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8721 (tm-30) REVERT: A 179 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8396 (tm-30) REVERT: A 195 LYS cc_start: 0.9582 (ttmt) cc_final: 0.8988 (tptt) REVERT: A 198 GLN cc_start: 0.9386 (tt0) cc_final: 0.9185 (tm-30) REVERT: A 200 GLU cc_start: 0.9224 (pp20) cc_final: 0.8891 (pp20) outliers start: 8 outliers final: 7 residues processed: 62 average time/residue: 0.2196 time to fit residues: 14.7636 Evaluate side-chains 64 residues out of total 163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 53 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.103994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.084495 restraints weight = 3969.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.086713 restraints weight = 1915.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.088069 restraints weight = 1227.716| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1590 Z= 0.214 Angle : 0.687 6.356 2134 Z= 0.337 Chirality : 0.032 0.121 236 Planarity : 0.003 0.028 284 Dihedral : 5.232 51.808 220 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.94 % Allowed : 28.40 % Favored : 66.67 % 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 (0.56), residues: 194 helix: 3.72 (0.35), residues: 172 sheet: None (None), residues: 0 loop : -1.00 (1.20), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 71 HIS 0.000 0.000 HIS A 100 PHE 0.004 0.001 PHE A 168 TYR 0.009 0.001 TYR A 129 ARG 0.006 0.001 ARG A 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 993.34 seconds wall clock time: 18 minutes 7.04 seconds (1087.04 seconds total)