Starting phenix.real_space_refine (version: dev) on Mon Feb 20 11:22:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap8_15561/02_2023/8ap8_15561.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap8_15561/02_2023/8ap8_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_15561/02_2023/8ap8_15561.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap8_15561/02_2023/8ap8_15561.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap8_15561/02_2023/8ap8_15561.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ap8_15561/02_2023/8ap8_15561.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 5.88, per 1000 atoms: 0.49 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: 10.09 Conformation dependent library (CDL) restraints added in 1.1 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: 0.31 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: 4.25 Time building geometry restraints manager: 10.45 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: 4699 17.81 - 35.61: 126 35.61 - 53.42: 10 53.42 - 71.23: 1 71.23 - 89.03: 3 Dihedral angle restraints: 4839 sinusoidal: 2360 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 4836 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 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. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.800 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: 38.090 Check model and map are aligned: 0.170 Process input model: 40.130 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 % 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 *********************** 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 : 1.045 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 outliers start: 2 outliers final: 2 residues processed: 162 average time/residue: 0.6534 time to fit residues: 125.1397 Evaluate side-chains 100 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1374 time to fit residues: 1.7773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8289 moved from start: 0.2171 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= 0.248 Angle : 0.472 5.298 8207 Z= 0.248 Chirality : 0.036 0.140 954 Planarity : 0.004 0.032 1062 Dihedral : 3.505 33.660 833 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 1.56 % 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: 2.28 (0.32), residues: 755 helix: 2.80 (0.23), residues: 495 sheet: -0.67 (0.64), residues: 62 loop : -1.25 (0.44), residues: 198 *********************** 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 110 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 1.006 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 outliers start: 10 outliers final: 6 residues processed: 105 average time/residue: 0.5145 time to fit residues: 66.7479 Evaluate side-chains 97 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2162 time to fit residues: 3.3300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 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: 0.8308 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 6071 Z= 0.252 Angle : 0.464 4.409 8207 Z= 0.244 Chirality : 0.037 0.139 954 Planarity : 0.003 0.033 1062 Dihedral : 3.558 33.896 833 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 0.78 % 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: 2.12 (0.32), residues: 755 helix: 2.71 (0.23), residues: 496 sheet: -1.11 (0.63), residues: 65 loop : -1.26 (0.45), residues: 194 *********************** 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 99 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 1.171 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 outliers start: 5 outliers final: 4 residues processed: 95 average time/residue: 0.4951 time to fit residues: 59.5779 Evaluate side-chains 95 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1478 time to fit residues: 2.3974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8331 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 6071 Z= 0.269 Angle : 0.472 4.430 8207 Z= 0.249 Chirality : 0.037 0.139 954 Planarity : 0.003 0.034 1062 Dihedral : 3.610 33.469 833 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.32), residues: 755 helix: 2.59 (0.23), residues: 496 sheet: -1.13 (0.64), residues: 65 loop : -1.30 (0.45), residues: 194 *********************** 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 99 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 1.060 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 outliers start: 8 outliers final: 5 residues processed: 94 average time/residue: 0.4829 time to fit residues: 57.3979 Evaluate side-chains 93 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1359 time to fit residues: 2.4605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.8345 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 6071 Z= 0.272 Angle : 0.474 4.420 8207 Z= 0.251 Chirality : 0.037 0.139 954 Planarity : 0.004 0.035 1062 Dihedral : 3.673 32.240 833 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.47 % 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: 1.91 (0.32), residues: 755 helix: 2.55 (0.23), residues: 496 sheet: -1.25 (0.64), residues: 65 loop : -1.34 (0.45), residues: 194 *********************** 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 93 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 90 average time/residue: 0.4786 time to fit residues: 54.2583 Evaluate side-chains 88 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1634 time to fit residues: 1.7927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.8361 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 6071 Z= 0.298 Angle : 0.490 4.430 8207 Z= 0.260 Chirality : 0.037 0.139 954 Planarity : 0.004 0.036 1062 Dihedral : 3.696 30.689 833 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.32), residues: 755 helix: 2.44 (0.23), residues: 495 sheet: -1.32 (0.63), residues: 65 loop : -1.38 (0.45), residues: 195 *********************** 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 96 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 1.058 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 outliers start: 9 outliers final: 6 residues processed: 89 average time/residue: 0.5116 time to fit residues: 57.5721 Evaluate side-chains 90 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1438 time to fit residues: 2.8432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 0.0970 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.8330 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 6071 Z= 0.182 Angle : 0.456 4.312 8207 Z= 0.238 Chirality : 0.036 0.141 954 Planarity : 0.003 0.034 1062 Dihedral : 3.581 27.469 833 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.32), residues: 755 helix: 2.63 (0.24), residues: 495 sheet: -1.29 (0.63), residues: 65 loop : -1.25 (0.46), residues: 195 *********************** 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 86 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.992 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 outliers start: 2 outliers final: 1 residues processed: 85 average time/residue: 0.4714 time to fit residues: 50.7551 Evaluate side-chains 84 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1318 time to fit residues: 1.4596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 13 optimal weight: 0.0980 chunk 45 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8334 moved from start: 0.3211 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= 0.201 Angle : 0.459 4.364 8207 Z= 0.239 Chirality : 0.036 0.140 954 Planarity : 0.003 0.034 1062 Dihedral : 3.520 24.035 833 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 1.09 % 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: 2.04 (0.32), residues: 755 helix: 2.67 (0.24), residues: 495 sheet: -1.24 (0.63), residues: 65 loop : -1.30 (0.45), residues: 195 *********************** 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 89 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.917 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 outliers start: 7 outliers final: 6 residues processed: 82 average time/residue: 0.4961 time to fit residues: 51.4054 Evaluate side-chains 88 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1466 time to fit residues: 2.7630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 68 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8329 moved from start: 0.3274 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= 0.200 Angle : 0.468 4.371 8207 Z= 0.245 Chirality : 0.036 0.140 954 Planarity : 0.003 0.037 1062 Dihedral : 3.477 19.987 833 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.00 % 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: 2.09 (0.32), residues: 755 helix: 2.70 (0.24), residues: 495 sheet: -1.19 (0.64), residues: 65 loop : -1.26 (0.46), residues: 195 *********************** 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 85 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.021 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 outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.5108 time to fit residues: 55.8831 Evaluate side-chains 82 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8335 moved from start: 0.3324 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= 0.213 Angle : 0.467 4.394 8207 Z= 0.245 Chirality : 0.036 0.139 954 Planarity : 0.003 0.035 1062 Dihedral : 3.458 17.245 833 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.47 % 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: 2.71 (0.24), residues: 495 sheet: -1.23 (0.64), residues: 65 loop : -1.25 (0.46), residues: 195 ********************** 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 85 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 1.150 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 outliers start: 3 outliers final: 3 residues processed: 82 average time/residue: 0.5065 time to fit residues: 52.4609 Evaluate side-chains 85 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.836 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1418 time to fit residues: 2.0998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 16 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.103903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.089064 restraints weight = 32719.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.092914 restraints weight = 15119.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.095374 restraints weight = 8843.452| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3382 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= 0.213 Angle : 0.470 4.444 8207 Z= 0.247 Chirality : 0.036 0.139 954 Planarity : 0.003 0.037 1062 Dihedral : 3.459 14.783 833 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 0.78 % 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: 2.09 (0.32), residues: 755 helix: 2.73 (0.23), residues: 495 sheet: -1.29 (0.66), residues: 64 loop : -1.33 (0.45), residues: 196 =============================================================================== Job complete usr+sys time: 3429.08 seconds wall clock time: 61 minutes 59.81 seconds (3719.81 seconds total)