Starting phenix.real_space_refine on Thu Sep 26 03:47:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap8_15561/09_2024/8ap8_15561.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap8_15561/09_2024/8ap8_15561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap8_15561/09_2024/8ap8_15561.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap8_15561/09_2024/8ap8_15561.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap8_15561/09_2024/8ap8_15561.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap8_15561/09_2024/8ap8_15561.cif" } resolution = 3.7 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= -0.001 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 11 5.16 5 C 3750 2.51 5 N 1064 2.21 5 O 1160 1.98 5 H 6098 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12083 Number of models: 1 Model: "" Number of chains: 5 Chain: "M" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 768 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "h" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2158 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "g" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 3953 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 8, 'TRANS': 259} Chain: "c" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 741 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "d" Number of atoms: 4463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 4463 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 15, 'TRANS': 254} Chain breaks: 1 Time building chain proxies: 9.03, per 1000 atoms: 0.75 Number of scatterers: 12083 At special positions: 0 Unit cell: (117.86, 87.15, 114.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 O 1160 8.00 N 1064 7.00 C 3750 6.00 H 6098 1.00 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: 3.19 Conformation dependent library (CDL) restraints added in 960.4 milliseconds 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1460 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 68.4% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'M' and resid 230 through 236 removed outlier: 3.564A pdb=" N LEU M 236 " --> pdb=" O GLU M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 254 Processing helix chain 'h' and resid 22 through 32 Processing helix chain 'h' and resid 44 through 52 Processing helix chain 'h' and resid 55 through 65 removed outlier: 3.560A pdb=" N LYS h 65 " --> pdb=" O SER h 61 " (cutoff:3.500A) Processing helix chain 'h' and resid 68 through 85 Processing helix chain 'h' and resid 88 through 96 Processing helix chain 'h' and resid 97 through 99 No H-bonds generated for 'chain 'h' and resid 97 through 99' Processing helix chain 'h' and resid 102 through 123 Processing helix chain 'h' and resid 124 through 139 Processing helix chain 'h' and resid 141 through 157 Processing helix chain 'g' and resid 13 through 29 Processing helix chain 'g' and resid 68 through 72 removed outlier: 3.542A pdb=" N SER g 72 " --> pdb=" O PRO g 69 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 104 removed outlier: 4.601A pdb=" N ASP g 98 " --> pdb=" O ARG g 94 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA g 101 " --> pdb=" O LEU g 97 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER g 102 " --> pdb=" O ASP g 98 " (cutoff:3.500A) Processing helix chain 'g' and resid 107 through 133 Processing helix chain 'g' and resid 149 through 166 removed outlier: 3.565A pdb=" N GLU g 160 " --> pdb=" O LYS g 156 " (cutoff:3.500A) Processing helix chain 'g' and resid 174 through 184 Processing helix chain 'g' and resid 185 through 188 Processing helix chain 'g' and resid 196 through 210 Processing helix chain 'g' and resid 230 through 246 Processing helix chain 'g' and resid 247 through 261 removed outlier: 3.666A pdb=" N ALA g 251 " --> pdb=" O LEU g 247 " (cutoff:3.500A) Processing helix chain 'g' and resid 264 through 269 Processing helix chain 'c' and resid 72 through 91 removed outlier: 3.865A pdb=" N THR c 91 " --> pdb=" O VAL c 87 " (cutoff:3.500A) Processing helix chain 'c' and resid 100 through 112 removed outlier: 3.959A pdb=" N VAL c 104 " --> pdb=" O ASP c 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 56 Processing helix chain 'd' and resid 69 through 85 Processing helix chain 'd' and resid 86 through 88 No H-bonds generated for 'chain 'd' and resid 86 through 88' Processing helix chain 'd' and resid 98 through 119 removed outlier: 3.792A pdb=" N ALA d 110 " --> pdb=" O CYS d 106 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU d 117 " --> pdb=" O SER d 113 " (cutoff:3.500A) Processing helix chain 'd' and resid 125 through 130 Processing helix chain 'd' and resid 133 through 164 Processing helix chain 'd' and resid 174 through 182 removed outlier: 3.562A pdb=" N SER d 180 " --> pdb=" O PRO d 176 " (cutoff:3.500A) Processing helix chain 'd' and resid 184 through 200 removed outlier: 4.473A pdb=" N VAL d 188 " --> pdb=" O ASP d 184 " (cutoff:3.500A) Processing helix chain 'd' and resid 206 through 218 removed outlier: 3.503A pdb=" N ILE d 210 " --> pdb=" O ASP d 206 " (cutoff:3.500A) Processing helix chain 'd' and resid 219 through 250 Proline residue: d 238 - end of helix Processing helix chain 'd' and resid 291 through 295 Processing helix chain 'd' and resid 301 through 324 removed outlier: 3.589A pdb=" N ASN d 324 " --> pdb=" O ALA d 320 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 226 through 227 removed outlier: 4.553A pdb=" N VAL M 226 " --> pdb=" O ARG d 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'g' and resid 32 through 37 removed outlier: 6.072A pdb=" N LYS g 3 " --> pdb=" O GLN g 33 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS g 35 " --> pdb=" O LYS g 3 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU g 5 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA g 37 " --> pdb=" O LEU g 5 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N PHE g 7 " --> pdb=" O ALA g 37 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL g 45 " --> pdb=" O GLN g 4 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR g 6 " --> pdb=" O VAL g 45 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL g 47 " --> pdb=" O THR g 6 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE g 8 " --> pdb=" O VAL g 47 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA g 44 " --> pdb=" O SER g 226 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLY g 228 " --> pdb=" O ALA g 44 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL g 46 " --> pdb=" O GLY g 228 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL g 216 " --> pdb=" O ALA g 58 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA g 58 " --> pdb=" O VAL g 216 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N HIS g 218 " --> pdb=" O HIS g 56 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N VAL g 190 " --> pdb=" O ARG g 136 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1152 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: 4.28 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6094 1.03 - 1.23: 4 1.23 - 1.42: 2410 1.42 - 1.61: 3643 1.61 - 1.81: 18 Bond restraints: 12169 Sorted by residual: bond pdb=" CB VAL h 152 " pdb=" CG1 VAL h 152 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.69e-01 bond pdb=" CB PRO g 185 " pdb=" CG PRO g 185 " ideal model delta sigma weight residual 1.492 1.521 -0.029 5.00e-02 4.00e+02 3.25e-01 bond pdb=" CG PRO d 296 " pdb=" CD PRO d 296 " ideal model delta sigma weight residual 1.503 1.486 0.017 3.40e-02 8.65e+02 2.62e-01 bond pdb=" C VAL g 172 " pdb=" O VAL g 172 " ideal model delta sigma weight residual 1.233 1.239 -0.006 1.25e-02 6.40e+03 2.49e-01 bond pdb=" CB ARG c 85 " pdb=" CG ARG c 85 " ideal model delta sigma weight residual 1.520 1.505 0.015 3.00e-02 1.11e+03 2.39e-01 ... (remaining 12164 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 20324 0.91 - 1.82: 1705 1.82 - 2.74: 40 2.74 - 3.65: 22 3.65 - 4.56: 9 Bond angle restraints: 22100 Sorted by residual: angle pdb=" C VAL g 79 " pdb=" N ARG g 80 " pdb=" CA ARG g 80 " ideal model delta sigma weight residual 122.72 120.49 2.23 1.38e+00 5.25e-01 2.60e+00 angle pdb=" C THR g 57 " pdb=" N ALA g 58 " pdb=" CA ALA g 58 " ideal model delta sigma weight residual 122.87 124.75 -1.88 1.44e+00 4.82e-01 1.70e+00 angle pdb=" C LEU g 193 " pdb=" N ASN g 194 " pdb=" CA ASN g 194 " ideal model delta sigma weight residual 120.97 118.69 2.28 1.82e+00 3.02e-01 1.56e+00 angle pdb=" C HIS g 56 " pdb=" N THR g 57 " pdb=" CA THR g 57 " ideal model delta sigma weight residual 122.62 120.79 1.83 1.56e+00 4.11e-01 1.38e+00 angle pdb=" C LEU d 295 " pdb=" N PRO d 296 " pdb=" CD PRO d 296 " ideal model delta sigma weight residual 125.00 129.56 -4.56 4.10e+00 5.95e-02 1.24e+00 ... (remaining 22095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5422 17.81 - 35.61: 171 35.61 - 53.42: 41 53.42 - 71.23: 12 71.23 - 89.03: 3 Dihedral angle restraints: 5649 sinusoidal: 3170 harmonic: 2479 Sorted by residual: dihedral pdb=" CA GLU d 204 " pdb=" CB GLU d 204 " pdb=" CG GLU d 204 " pdb=" CD GLU d 204 " ideal model delta sinusoidal sigma weight residual -60.00 -113.64 53.64 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N ASP M 247 " pdb=" CA ASP M 247 " pdb=" CB ASP M 247 " pdb=" CG ASP M 247 " ideal model delta sinusoidal sigma weight residual 180.00 132.09 47.91 3 1.50e+01 4.44e-03 8.56e+00 dihedral pdb=" CA THR g 57 " pdb=" C THR g 57 " pdb=" N ALA g 58 " pdb=" CA ALA g 58 " ideal model delta harmonic sigma weight residual -180.00 -165.54 -14.46 0 5.00e+00 4.00e-02 8.36e+00 ... (remaining 5646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 670 0.029 - 0.058: 183 0.058 - 0.086: 57 0.086 - 0.115: 38 0.115 - 0.144: 6 Chirality restraints: 954 Sorted by residual: chirality pdb=" CA VAL d 58 " pdb=" N VAL d 58 " pdb=" C VAL d 58 " pdb=" CB VAL d 58 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE g 8 " pdb=" N ILE g 8 " pdb=" C ILE g 8 " pdb=" CB ILE g 8 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA VAL g 196 " pdb=" N VAL g 196 " pdb=" C VAL g 196 " pdb=" CB VAL g 196 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 951 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA g 58 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C ALA g 58 " 0.065 2.00e-02 2.50e+03 pdb=" O ALA g 58 " -0.025 2.00e-02 2.50e+03 pdb=" N VAL g 59 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP d 175 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO d 176 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO d 176 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO d 176 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS d 237 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO d 238 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO d 238 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO d 238 " 0.015 5.00e-02 4.00e+02 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 1024 2.24 - 2.83: 28368 2.83 - 3.42: 29681 3.42 - 4.01: 39555 4.01 - 4.60: 63427 Nonbonded interactions: 162055 Sorted by model distance: nonbonded pdb=" HE ARG g 80 " pdb=" OE1 GLU g 203 " model vdw 1.654 2.450 nonbonded pdb="HH22 ARG g 31 " pdb=" OE2 GLU g 250 " model vdw 1.684 2.450 nonbonded pdb=" O VAL g 196 " pdb=" HG1 THR g 199 " model vdw 1.709 2.450 nonbonded pdb=" OE2 GLU g 61 " pdb=" HZ2 LYS g 128 " model vdw 1.737 2.450 nonbonded pdb=" HE1 TRP h 140 " pdb=" O SER d 21 " model vdw 1.746 2.450 ... (remaining 162050 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 7.520 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: 0.240 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.740 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.002 0.029 6071 Z= 0.156 Angle : 0.386 4.562 8207 Z= 0.202 Chirality : 0.035 0.144 954 Planarity : 0.003 0.038 1062 Dihedral : 8.105 89.035 2312 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.31 % Allowed : 2.18 % Favored : 97.51 % 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: 2.44 (0.32), residues: 755 helix: 3.01 (0.24), residues: 489 sheet: -0.92 (0.61), residues: 62 loop : -1.17 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 112 HIS 0.003 0.001 HIS g 56 PHE 0.006 0.001 PHE h 52 TYR 0.005 0.001 TYR h 87 ARG 0.001 0.000 ARG c 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 250 GLU cc_start: 0.8287 (tt0) cc_final: 0.7949 (tt0) REVERT: h 45 ASP cc_start: 0.8277 (t70) cc_final: 0.8011 (t0) REVERT: h 146 LYS cc_start: 0.8520 (tttt) cc_final: 0.8250 (mtmm) REVERT: c 86 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7681 (ttm-80) REVERT: c 113 ASN cc_start: 0.8286 (m110) cc_final: 0.8070 (m-40) REVERT: d 170 VAL cc_start: 0.9214 (t) cc_final: 0.8991 (p) outliers start: 2 outliers final: 2 residues processed: 162 average time/residue: 0.6635 time to fit residues: 126.8896 Evaluate side-chains 101 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 247 ASP Chi-restraints excluded: chain g residue 60 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6071 Z= 0.231 Angle : 0.470 5.216 8207 Z= 0.248 Chirality : 0.037 0.139 954 Planarity : 0.004 0.034 1062 Dihedral : 3.930 47.743 836 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.56 % Allowed : 5.76 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.32), residues: 755 helix: 2.83 (0.23), residues: 495 sheet: -0.72 (0.64), residues: 61 loop : -1.29 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 175 HIS 0.003 0.001 HIS g 56 PHE 0.013 0.001 PHE c 74 TYR 0.011 0.001 TYR M 214 ARG 0.003 0.000 ARG d 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 146 LYS cc_start: 0.8669 (tttt) cc_final: 0.8391 (mtmm) REVERT: g 33 GLN cc_start: 0.7863 (mt0) cc_final: 0.7450 (mm-40) REVERT: c 86 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7733 (ttm-80) REVERT: c 113 ASN cc_start: 0.8349 (m110) cc_final: 0.8139 (m-40) REVERT: d 304 GLU cc_start: 0.7916 (tp30) cc_final: 0.7708 (tp30) outliers start: 10 outliers final: 6 residues processed: 109 average time/residue: 0.4940 time to fit residues: 67.0020 Evaluate side-chains 101 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 247 ASP Chi-restraints excluded: chain h residue 39 ASN Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 245 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8217 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6071 Z= 0.255 Angle : 0.470 4.293 8207 Z= 0.248 Chirality : 0.037 0.139 954 Planarity : 0.004 0.034 1062 Dihedral : 3.984 48.098 836 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.87 % Allowed : 7.63 % Favored : 90.50 % 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: 2.08 (0.32), residues: 755 helix: 2.69 (0.23), residues: 496 sheet: -1.30 (0.62), residues: 65 loop : -1.26 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 175 HIS 0.004 0.001 HIS c 103 PHE 0.012 0.001 PHE c 74 TYR 0.013 0.001 TYR M 214 ARG 0.005 0.000 ARG d 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 146 LYS cc_start: 0.8638 (tttt) cc_final: 0.8380 (mtmm) REVERT: c 86 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7772 (ttm-80) REVERT: c 113 ASN cc_start: 0.8324 (m110) cc_final: 0.8095 (m-40) outliers start: 12 outliers final: 10 residues processed: 103 average time/residue: 0.4762 time to fit residues: 61.8227 Evaluate side-chains 105 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 210 ASP Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 247 ASP Chi-restraints excluded: chain h residue 39 ASN Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain g residue 179 ASN Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 245 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8237 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6071 Z= 0.263 Angle : 0.473 4.232 8207 Z= 0.251 Chirality : 0.037 0.139 954 Planarity : 0.004 0.038 1062 Dihedral : 4.024 47.914 836 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.02 % Allowed : 8.41 % Favored : 89.56 % 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: 1.99 (0.32), residues: 755 helix: 2.63 (0.23), residues: 495 sheet: -1.38 (0.62), residues: 65 loop : -1.28 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 175 HIS 0.004 0.001 HIS g 229 PHE 0.011 0.001 PHE c 74 TYR 0.008 0.001 TYR d 217 ARG 0.005 0.000 ARG d 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 146 LYS cc_start: 0.8662 (tttt) cc_final: 0.8375 (mtmm) REVERT: g 33 GLN cc_start: 0.7846 (mt0) cc_final: 0.7533 (mp10) REVERT: g 180 GLN cc_start: 0.8847 (tt0) cc_final: 0.8597 (tt0) REVERT: c 86 ARG cc_start: 0.8064 (ttm-80) cc_final: 0.7783 (ttm-80) REVERT: c 113 ASN cc_start: 0.8351 (m110) cc_final: 0.8116 (m-40) outliers start: 13 outliers final: 11 residues processed: 101 average time/residue: 0.4994 time to fit residues: 64.1099 Evaluate side-chains 102 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 247 ASP Chi-restraints excluded: chain h residue 39 ASN Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 59 GLU Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain g residue 70 LEU Chi-restraints excluded: chain g residue 179 ASN Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 245 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8253 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6071 Z= 0.274 Angle : 0.482 4.224 8207 Z= 0.256 Chirality : 0.037 0.139 954 Planarity : 0.004 0.044 1062 Dihedral : 4.047 46.759 836 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.02 % Allowed : 9.35 % Favored : 88.63 % 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: 1.89 (0.32), residues: 755 helix: 2.58 (0.24), residues: 495 sheet: -1.51 (0.62), residues: 65 loop : -1.34 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 175 HIS 0.005 0.001 HIS g 229 PHE 0.012 0.001 PHE c 74 TYR 0.009 0.001 TYR d 217 ARG 0.006 0.000 ARG d 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 146 LYS cc_start: 0.8651 (tttt) cc_final: 0.8360 (mtmm) REVERT: c 86 ARG cc_start: 0.8106 (ttm-80) cc_final: 0.7853 (ttm-80) REVERT: c 113 ASN cc_start: 0.8352 (m110) cc_final: 0.8115 (m-40) outliers start: 13 outliers final: 11 residues processed: 97 average time/residue: 0.4845 time to fit residues: 59.0710 Evaluate side-chains 96 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 210 ASP Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 247 ASP Chi-restraints excluded: chain h residue 39 ASN Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 59 GLU Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain g residue 179 ASN Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 245 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 chunk 37 optimal weight: 0.1980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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: 0.8227 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6071 Z= 0.184 Angle : 0.456 4.087 8207 Z= 0.239 Chirality : 0.036 0.139 954 Planarity : 0.004 0.045 1062 Dihedral : 3.894 45.605 836 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.18 % Allowed : 9.35 % Favored : 88.47 % 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: 2.11 (0.33), residues: 755 helix: 2.74 (0.24), residues: 496 sheet: -1.56 (0.61), residues: 65 loop : -1.20 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 175 HIS 0.003 0.001 HIS c 103 PHE 0.011 0.001 PHE c 74 TYR 0.009 0.001 TYR h 87 ARG 0.007 0.000 ARG d 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 245 GLN cc_start: 0.8496 (tp40) cc_final: 0.8245 (tp40) REVERT: h 146 LYS cc_start: 0.8644 (tttt) cc_final: 0.8356 (mtmm) REVERT: g 18 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7806 (tm-30) REVERT: g 180 GLN cc_start: 0.8835 (tt0) cc_final: 0.8519 (tt0) REVERT: c 86 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7809 (ttm-80) REVERT: c 113 ASN cc_start: 0.8343 (m110) cc_final: 0.8085 (m-40) REVERT: d 304 GLU cc_start: 0.7909 (tp30) cc_final: 0.7667 (tp30) outliers start: 14 outliers final: 12 residues processed: 94 average time/residue: 0.4783 time to fit residues: 56.7291 Evaluate side-chains 97 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 247 ASP Chi-restraints excluded: chain h residue 39 ASN Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 59 GLU Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain g residue 70 LEU Chi-restraints excluded: chain g residue 179 ASN Chi-restraints excluded: chain c residue 106 ASP Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 245 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8240 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6071 Z= 0.234 Angle : 0.466 4.163 8207 Z= 0.246 Chirality : 0.036 0.139 954 Planarity : 0.004 0.046 1062 Dihedral : 3.888 45.152 836 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.18 % Allowed : 9.19 % Favored : 88.63 % 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: 2.05 (0.32), residues: 755 helix: 2.69 (0.24), residues: 496 sheet: -1.55 (0.61), residues: 65 loop : -1.22 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 175 HIS 0.004 0.001 HIS g 229 PHE 0.012 0.001 PHE c 74 TYR 0.007 0.001 TYR d 217 ARG 0.007 0.000 ARG d 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 146 LYS cc_start: 0.8646 (tttt) cc_final: 0.8347 (mtmm) REVERT: c 113 ASN cc_start: 0.8354 (m110) cc_final: 0.8095 (m-40) outliers start: 14 outliers final: 13 residues processed: 90 average time/residue: 0.4844 time to fit residues: 54.9039 Evaluate side-chains 96 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 247 ASP Chi-restraints excluded: chain h residue 39 ASN Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 59 GLU Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain g residue 179 ASN Chi-restraints excluded: chain c residue 106 ASP Chi-restraints excluded: chain d residue 103 MET Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 245 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.0670 chunk 35 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 overall best weight: 0.3318 ------------------------------------------------------------------------------- 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: 0.8212 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6071 Z= 0.159 Angle : 0.462 4.914 8207 Z= 0.240 Chirality : 0.036 0.140 954 Planarity : 0.004 0.051 1062 Dihedral : 3.763 43.859 836 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.18 % Allowed : 9.81 % Favored : 88.01 % 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: 2.24 (0.33), residues: 755 helix: 2.81 (0.24), residues: 496 sheet: -1.55 (0.61), residues: 65 loop : -1.06 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 175 HIS 0.003 0.001 HIS c 103 PHE 0.012 0.001 PHE c 74 TYR 0.007 0.001 TYR g 217 ARG 0.008 0.000 ARG d 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 146 LYS cc_start: 0.8660 (tttt) cc_final: 0.8351 (mtmm) REVERT: g 18 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7811 (tm-30) REVERT: c 113 ASN cc_start: 0.8359 (m110) cc_final: 0.8159 (m110) outliers start: 14 outliers final: 14 residues processed: 96 average time/residue: 0.4731 time to fit residues: 57.1909 Evaluate side-chains 99 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 247 ASP Chi-restraints excluded: chain h residue 39 ASN Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 59 GLU Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain g residue 70 LEU Chi-restraints excluded: chain g residue 179 ASN Chi-restraints excluded: chain c residue 106 ASP Chi-restraints excluded: chain d residue 103 MET Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 245 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 68 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.0970 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6071 Z= 0.186 Angle : 0.475 5.239 8207 Z= 0.248 Chirality : 0.036 0.140 954 Planarity : 0.004 0.035 1062 Dihedral : 3.738 43.251 836 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.34 % Allowed : 10.28 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.33), residues: 755 helix: 2.81 (0.23), residues: 496 sheet: -1.54 (0.62), residues: 65 loop : -1.05 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 175 HIS 0.003 0.001 HIS c 103 PHE 0.012 0.001 PHE c 74 TYR 0.013 0.001 TYR h 87 ARG 0.007 0.000 ARG d 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 245 GLN cc_start: 0.8571 (tp40) cc_final: 0.8348 (tp40) REVERT: h 146 LYS cc_start: 0.8664 (tttt) cc_final: 0.8351 (mtmm) REVERT: g 18 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7833 (tm-30) REVERT: c 113 ASN cc_start: 0.8377 (m110) cc_final: 0.8176 (m110) outliers start: 15 outliers final: 13 residues processed: 93 average time/residue: 0.4461 time to fit residues: 52.6772 Evaluate side-chains 98 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 247 ASP Chi-restraints excluded: chain h residue 39 ASN Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 59 GLU Chi-restraints excluded: chain h residue 119 VAL Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain g residue 179 ASN Chi-restraints excluded: chain c residue 106 ASP Chi-restraints excluded: chain d residue 103 MET Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 245 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6071 Z= 0.256 Angle : 0.505 5.520 8207 Z= 0.267 Chirality : 0.037 0.138 954 Planarity : 0.004 0.036 1062 Dihedral : 3.803 43.084 836 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.18 % Allowed : 10.75 % Favored : 87.07 % 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: 2.13 (0.32), residues: 755 helix: 2.72 (0.24), residues: 496 sheet: -1.43 (0.62), residues: 62 loop : -1.15 (0.47), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 175 HIS 0.004 0.001 HIS g 229 PHE 0.013 0.001 PHE c 74 TYR 0.009 0.001 TYR M 214 ARG 0.006 0.000 ARG d 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 245 GLN cc_start: 0.8589 (tp40) cc_final: 0.8269 (tp40) REVERT: h 146 LYS cc_start: 0.8688 (tttt) cc_final: 0.8360 (mtmm) REVERT: c 113 ASN cc_start: 0.8395 (m110) cc_final: 0.8191 (m110) outliers start: 14 outliers final: 13 residues processed: 91 average time/residue: 0.4646 time to fit residues: 53.8577 Evaluate side-chains 95 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 247 ASP Chi-restraints excluded: chain h residue 39 ASN Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 59 GLU Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain g residue 179 ASN Chi-restraints excluded: chain c residue 106 ASP Chi-restraints excluded: chain d residue 103 MET Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 245 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.0470 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7878 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.116849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.100746 restraints weight = 33251.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.104902 restraints weight = 14876.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107543 restraints weight = 8687.181| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6071 Z= 0.246 Angle : 0.489 4.955 8207 Z= 0.260 Chirality : 0.037 0.138 954 Planarity : 0.004 0.036 1062 Dihedral : 3.823 42.615 836 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.02 % Allowed : 10.59 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.32), residues: 755 helix: 2.68 (0.23), residues: 496 sheet: -1.55 (0.62), residues: 62 loop : -1.16 (0.46), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 175 HIS 0.004 0.001 HIS g 229 PHE 0.013 0.001 PHE c 74 TYR 0.010 0.001 TYR h 87 ARG 0.007 0.000 ARG d 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3492.27 seconds wall clock time: 62 minutes 47.79 seconds (3767.79 seconds total)