Starting phenix.real_space_refine on Fri Mar 15 15:29:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap8_15561/03_2024/8ap8_15561.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap8_15561/03_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_15561/03_2024/8ap8_15561.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap8_15561/03_2024/8ap8_15561.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap8_15561/03_2024/8ap8_15561.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap8_15561/03_2024/8ap8_15561.pdb" } 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 Residue "g PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.56, per 1000 atoms: 0.46 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.60 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.89 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: 4.33 Time building geometry restraints manager: 9.96 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: 100.68 - 107.34: 267 107.34 - 114.00: 15067 114.00 - 120.66: 4035 120.66 - 127.32: 2675 127.32 - 133.99: 56 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 1.850 nonbonded pdb="HH22 ARG g 31 " pdb=" OE2 GLU g 250 " model vdw 1.684 1.850 nonbonded pdb=" O VAL g 196 " pdb=" HG1 THR g 199 " model vdw 1.709 1.850 nonbonded pdb=" OE2 GLU g 61 " pdb=" HZ2 LYS g 128 " model vdw 1.737 1.850 nonbonded pdb=" HE1 TRP h 140 " pdb=" O SER d 21 " model vdw 1.746 1.850 ... (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 ========== 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: 13.490 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: 0.190 Extract box with map and model: 35.270 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 40.530 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.790 ------------------------------------------------------------------------------- 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 : 0.993 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: 0.6427 time to fit residues: 123.7218 Evaluate side-chains 101 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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: 0.5980 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8193 moved from start: 0.2055 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= 0.260 Angle : 0.472 4.968 8207 Z= 0.250 Chirality : 0.036 0.139 954 Planarity : 0.004 0.034 1062 Dihedral : 3.980 47.889 836 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.71 % Allowed : 5.45 % Favored : 92.83 % 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: 2.27 (0.32), residues: 755 helix: 2.82 (0.23), residues: 495 sheet: -1.06 (0.63), residues: 66 loop : -1.15 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 175 HIS 0.003 0.001 HIS g 229 PHE 0.012 0.001 PHE c 74 TYR 0.010 0.001 TYR M 214 ARG 0.004 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 111 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 1.086 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: 0.8664 (tttt) cc_final: 0.8406 (mtmm) REVERT: c 86 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7742 (ttm-80) outliers start: 11 outliers final: 8 residues processed: 106 average time/residue: 0.5186 time to fit residues: 67.8965 Evaluate side-chains 99 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 247 ASP Chi-restraints excluded: chain h residue 29 LYS 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 g residue 89 ASP 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: 0.9980 chunk 20 optimal weight: 0.2980 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: 0.9990 chunk 59 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8209 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6071 Z= 0.237 Angle : 0.459 4.272 8207 Z= 0.240 Chirality : 0.036 0.139 954 Planarity : 0.003 0.034 1062 Dihedral : 4.038 47.997 836 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 2.17 (0.32), residues: 755 helix: 2.74 (0.23), residues: 496 sheet: -1.08 (0.64), residues: 65 loop : -1.21 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 175 HIS 0.005 0.001 HIS c 103 PHE 0.012 0.001 PHE c 74 TYR 0.008 0.001 TYR d 217 ARG 0.004 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 108 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.978 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: h 146 LYS cc_start: 0.8638 (tttt) cc_final: 0.8381 (mtmm) REVERT: c 86 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7770 (ttm-80) outliers start: 12 outliers final: 10 residues processed: 101 average time/residue: 0.4655 time to fit residues: 59.4131 Evaluate side-chains 103 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 210 ASP 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 89 ASP 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: 0.8980 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 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: 0.8233 moved from start: 0.2618 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= 0.257 Angle : 0.463 4.237 8207 Z= 0.245 Chirality : 0.037 0.139 954 Planarity : 0.003 0.034 1062 Dihedral : 4.067 47.961 836 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.18 % Allowed : 8.10 % Favored : 89.72 % 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: 2.06 (0.32), residues: 755 helix: 2.65 (0.23), residues: 496 sheet: -1.12 (0.64), 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 g 229 PHE 0.011 0.001 PHE c 74 TYR 0.009 0.001 TYR d 217 ARG 0.004 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 103 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.978 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: M 214 TYR cc_start: 0.8546 (m-10) cc_final: 0.8247 (m-10) REVERT: h 146 LYS cc_start: 0.8653 (tttt) cc_final: 0.8367 (mtmm) REVERT: g 18 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7799 (tm-30) REVERT: c 86 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7789 (ttm-80) REVERT: d 204 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7689 (mm-30) outliers start: 14 outliers final: 11 residues processed: 97 average time/residue: 0.4675 time to fit residues: 57.3261 Evaluate side-chains 98 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 89 ASP 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: 0.9980 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8242 moved from start: 0.2876 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= 0.245 Angle : 0.459 4.192 8207 Z= 0.242 Chirality : 0.037 0.139 954 Planarity : 0.003 0.035 1062 Dihedral : 4.048 46.137 836 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.87 % Allowed : 9.35 % Favored : 88.79 % 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: 2.02 (0.32), residues: 755 helix: 2.64 (0.23), residues: 496 sheet: -1.19 (0.64), residues: 65 loop : -1.31 (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 g 229 PHE 0.012 0.001 PHE c 74 TYR 0.008 0.001 TYR g 217 ARG 0.003 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 98 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 1.067 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: 0.8643 (tttt) cc_final: 0.8358 (mtmm) REVERT: g 18 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7762 (tm-30) REVERT: c 86 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7839 (ttm-80) outliers start: 12 outliers final: 10 residues processed: 93 average time/residue: 0.4706 time to fit residues: 55.2530 Evaluate side-chains 93 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 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 89 ASP 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: 0.9990 chunk 64 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8261 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6071 Z= 0.282 Angle : 0.471 4.243 8207 Z= 0.250 Chirality : 0.037 0.140 954 Planarity : 0.004 0.036 1062 Dihedral : 4.069 45.542 836 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.34 % Allowed : 9.03 % 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: 1.92 (0.32), residues: 755 helix: 2.57 (0.23), residues: 495 sheet: -1.26 (0.64), residues: 65 loop : -1.32 (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 0.003 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 102 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.831 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 214 TYR cc_start: 0.8564 (m-10) cc_final: 0.8311 (m-10) REVERT: h 146 LYS cc_start: 0.8652 (tttt) cc_final: 0.8358 (mtmm) REVERT: g 18 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7766 (tm-30) REVERT: c 86 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7844 (ttm-80) REVERT: c 98 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7392 (tm-30) outliers start: 15 outliers final: 12 residues processed: 94 average time/residue: 0.4871 time to fit residues: 58.1024 Evaluate side-chains 96 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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 89 ASP Chi-restraints excluded: chain g residue 179 ASN Chi-restraints excluded: chain c residue 87 VAL 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: 0.7980 chunk 8 optimal weight: 0.0020 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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: 0.8228 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6071 Z= 0.173 Angle : 0.440 4.108 8207 Z= 0.229 Chirality : 0.036 0.140 954 Planarity : 0.003 0.035 1062 Dihedral : 3.941 44.262 836 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.34 % Allowed : 9.35 % Favored : 88.32 % 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: 2.16 (0.32), residues: 755 helix: 2.77 (0.23), residues: 496 sheet: -1.33 (0.63), residues: 65 loop : -1.22 (0.46), 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 0.011 0.001 PHE c 74 TYR 0.008 0.001 TYR g 217 ARG 0.002 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 99 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.982 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: M 214 TYR cc_start: 0.8545 (m-10) cc_final: 0.8315 (m-10) REVERT: h 146 LYS cc_start: 0.8646 (tttt) cc_final: 0.8341 (mtmm) REVERT: g 18 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7865 (tm-30) REVERT: c 86 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.7784 (ttm-80) REVERT: c 98 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7443 (tm-30) REVERT: d 304 GLU cc_start: 0.7896 (tp30) cc_final: 0.7635 (tp30) outliers start: 15 outliers final: 10 residues processed: 90 average time/residue: 0.4702 time to fit residues: 53.5036 Evaluate side-chains 93 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 210 ASP 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 89 ASP 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: 2.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 6 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.8226 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6071 Z= 0.183 Angle : 0.446 4.354 8207 Z= 0.232 Chirality : 0.036 0.140 954 Planarity : 0.003 0.035 1062 Dihedral : 3.879 43.737 836 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.87 % Allowed : 9.81 % Favored : 88.32 % 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: 2.22 (0.32), residues: 755 helix: 2.80 (0.23), residues: 496 sheet: -1.28 (0.64), residues: 65 loop : -1.18 (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 0.010 0.001 PHE c 74 TYR 0.007 0.001 TYR g 217 ARG 0.002 0.000 ARG g 243 *********************** 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 95 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 1.011 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: M 214 TYR cc_start: 0.8547 (m-10) cc_final: 0.8327 (m-10) REVERT: h 146 LYS cc_start: 0.8673 (tttt) cc_final: 0.8358 (mtmm) REVERT: g 18 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7864 (tm-30) REVERT: d 304 GLU cc_start: 0.7919 (tp30) cc_final: 0.7688 (tp30) outliers start: 12 outliers final: 11 residues processed: 88 average time/residue: 0.4781 time to fit residues: 53.1389 Evaluate side-chains 94 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 45 ASP 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 89 ASP Chi-restraints excluded: chain g residue 179 ASN 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: 0.1980 chunk 66 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.8218 moved from start: 0.3118 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= 0.170 Angle : 0.456 4.867 8207 Z= 0.236 Chirality : 0.036 0.140 954 Planarity : 0.004 0.046 1062 Dihedral : 3.817 43.364 836 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.87 % Allowed : 10.28 % Favored : 87.85 % 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: 2.28 (0.33), residues: 755 helix: 2.83 (0.23), residues: 496 sheet: -1.29 (0.64), residues: 65 loop : -1.11 (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 0.010 0.001 PHE c 74 TYR 0.007 0.001 TYR g 217 ARG 0.006 0.000 ARG c 86 *********************** 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 100 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 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: M 214 TYR cc_start: 0.8557 (m-10) cc_final: 0.8349 (m-10) REVERT: h 146 LYS cc_start: 0.8669 (tttt) cc_final: 0.8348 (mtmm) REVERT: g 18 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7718 (tm-30) REVERT: d 304 GLU cc_start: 0.7894 (tp30) cc_final: 0.7639 (tp30) outliers start: 12 outliers final: 10 residues processed: 93 average time/residue: 0.4611 time to fit residues: 54.3244 Evaluate side-chains 93 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 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 89 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: 0.0670 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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: 0.8226 moved from start: 0.3165 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= 0.198 Angle : 0.461 5.465 8207 Z= 0.242 Chirality : 0.036 0.142 954 Planarity : 0.003 0.035 1062 Dihedral : 3.805 43.133 836 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.02 % Allowed : 10.12 % Favored : 87.85 % 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: 2.25 (0.33), residues: 755 helix: 2.81 (0.23), residues: 496 sheet: -1.34 (0.64), residues: 65 loop : -1.09 (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 g 229 PHE 0.013 0.001 PHE c 74 TYR 0.007 0.001 TYR g 217 ARG 0.003 0.000 ARG c 86 ********************** 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 97 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 1.061 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: h 146 LYS cc_start: 0.8676 (tttt) cc_final: 0.8356 (mtmm) REVERT: g 18 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7864 (tm-30) REVERT: d 173 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8872 (tp) outliers start: 13 outliers final: 9 residues processed: 90 average time/residue: 0.4751 time to fit residues: 55.2969 Evaluate side-chains 95 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 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 89 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: 2.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.118480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102667 restraints weight = 33314.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106776 restraints weight = 14913.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.109333 restraints weight = 8666.953| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3290 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= 0.281 Angle : 0.495 4.707 8207 Z= 0.263 Chirality : 0.037 0.138 954 Planarity : 0.004 0.036 1062 Dihedral : 3.904 43.434 836 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.02 % Allowed : 10.44 % Favored : 87.54 % 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: 2.03 (0.32), residues: 755 helix: 2.65 (0.23), residues: 495 sheet: -1.46 (0.64), residues: 65 loop : -1.16 (0.46), residues: 195 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 0.016 0.001 TYR M 253 ARG 0.002 0.000 ARG c 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3473.23 seconds wall clock time: 62 minutes 0.17 seconds (3720.17 seconds total)