Starting phenix.real_space_refine on Mon Mar 11 15:36:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr9_16805/03_2024/8cr9_16805.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr9_16805/03_2024/8cr9_16805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr9_16805/03_2024/8cr9_16805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr9_16805/03_2024/8cr9_16805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr9_16805/03_2024/8cr9_16805.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cr9_16805/03_2024/8cr9_16805.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 2730 2.51 5 N 736 2.21 5 O 872 1.98 5 H 4272 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 145": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 163": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 8621 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3300 Classifications: {'peptide': 222} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 209} Chain: "B" Number of atoms: 3290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3290 Classifications: {'peptide': 217} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205} Chain: "C" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2031 Classifications: {'peptide': 132} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 124} Time building chain proxies: 4.62, per 1000 atoms: 0.54 Number of scatterers: 8621 At special positions: 0 Unit cell: (64.6, 82.45, 105.4, 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 872 8.00 N 736 7.00 C 2730 6.00 H 4272 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: 7.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1054 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 10 sheets defined 21.7% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.918A pdb=" N VAL A 48 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA A 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 49' Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 210 through 213 Processing helix chain 'B' and resid 124 through 130 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'C' and resid 130 through 130 No H-bonds generated for 'chain 'C' and resid 130 through 130' Processing helix chain 'C' and resid 131 through 158 Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 184 through 189 removed outlier: 4.243A pdb=" N ASP C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 removed outlier: 3.797A pdb=" N LEU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 235 through 261 removed outlier: 3.587A pdb=" N ARG C 247 " --> pdb=" O THR C 243 " (cutoff:3.500A) Proline residue: C 250 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 3.717A pdb=" N LEU A 18 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 39 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 133 removed outlier: 4.841A pdb=" N ALA A 146 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 193 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLY A 148 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A 191 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU A 150 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER A 189 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS A 152 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 187 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.668A pdb=" N THR A 214 " --> pdb=" O HIS A 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 7 removed outlier: 5.210A pdb=" N ASP B 17 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AA8, first strand: chain 'B' and resid 117 through 121 removed outlier: 4.296A pdb=" N SER B 134 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 177 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 179 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER B 165 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 163 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 157 Processing sheet with id=AB1, first strand: chain 'C' and resid 162 through 163 149 hydrogen bonds defined for protein. 390 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: 2.84 Time building geometry restraints manager: 7.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 4263 1.11 - 1.29: 731 1.29 - 1.47: 1478 1.47 - 1.64: 2230 1.64 - 1.82: 13 Bond restraints: 8715 Sorted by residual: bond pdb=" N LEU C 261 " pdb=" H LEU C 261 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CD1 TYR A 94 " pdb=" HD1 TYR A 94 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CD2 TYR A 95 " pdb=" HD2 TYR A 95 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CE1 TYR B 176 " pdb=" HE1 TYR B 176 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CE1 TYR A 94 " pdb=" HE1 TYR A 94 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 8710 not shown) Histogram of bond angle deviations from ideal: 95.98 - 103.86: 81 103.86 - 111.74: 9305 111.74 - 119.61: 3450 119.61 - 127.49: 2830 127.49 - 135.36: 65 Bond angle restraints: 15731 Sorted by residual: angle pdb=" N VAL B 83 " pdb=" CA VAL B 83 " pdb=" C VAL B 83 " ideal model delta sigma weight residual 112.17 119.58 -7.41 9.50e-01 1.11e+00 6.08e+01 angle pdb=" C TRP A 47 " pdb=" N VAL A 48 " pdb=" CA VAL A 48 " ideal model delta sigma weight residual 120.60 129.62 -9.02 1.29e+00 6.01e-01 4.89e+01 angle pdb=" CA PHE B 101 " pdb=" CB PHE B 101 " pdb=" CG PHE B 101 " ideal model delta sigma weight residual 113.80 120.28 -6.48 1.00e+00 1.00e+00 4.20e+01 angle pdb=" N TYR B 94 " pdb=" CA TYR B 94 " pdb=" C TYR B 94 " ideal model delta sigma weight residual 108.60 116.67 -8.07 1.46e+00 4.69e-01 3.06e+01 angle pdb=" N VAL A 48 " pdb=" CA VAL A 48 " pdb=" C VAL A 48 " ideal model delta sigma weight residual 110.36 116.06 -5.70 1.05e+00 9.07e-01 2.95e+01 ... (remaining 15726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3766 17.70 - 35.41: 277 35.41 - 53.11: 90 53.11 - 70.81: 17 70.81 - 88.51: 8 Dihedral angle restraints: 4158 sinusoidal: 2253 harmonic: 1905 Sorted by residual: dihedral pdb=" CA ASP A 110 " pdb=" C ASP A 110 " pdb=" N SER A 111 " pdb=" CA SER A 111 " ideal model delta harmonic sigma weight residual -180.00 -150.82 -29.18 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA CYS B 88 " pdb=" C CYS B 88 " pdb=" N GLN B 89 " pdb=" CA GLN B 89 " ideal model delta harmonic sigma weight residual 180.00 150.84 29.16 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA PHE B 142 " pdb=" C PHE B 142 " pdb=" N TYR B 143 " pdb=" CA TYR B 143 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 4155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 401 0.087 - 0.174: 234 0.174 - 0.262: 36 0.262 - 0.349: 7 0.349 - 0.436: 3 Chirality restraints: 681 Sorted by residual: chirality pdb=" CA HIS B 96 " pdb=" N HIS B 96 " pdb=" C HIS B 96 " pdb=" CB HIS B 96 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CA LYS B 50 " pdb=" N LYS B 50 " pdb=" C LYS B 50 " pdb=" CB LYS B 50 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA LYS C 258 " pdb=" N LYS C 258 " pdb=" C LYS C 258 " pdb=" CB LYS C 258 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 678 not shown) Planarity restraints: 1317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 90 " 0.203 2.00e-02 2.50e+03 7.80e-02 1.83e+02 pdb=" CG TYR B 90 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR B 90 " -0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR B 90 " -0.068 2.00e-02 2.50e+03 pdb=" CE1 TYR B 90 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR B 90 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR B 90 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 90 " 0.113 2.00e-02 2.50e+03 pdb=" HD1 TYR B 90 " -0.036 2.00e-02 2.50e+03 pdb=" HD2 TYR B 90 " -0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR B 90 " 0.007 2.00e-02 2.50e+03 pdb=" HE2 TYR B 90 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 59 " 0.195 2.00e-02 2.50e+03 7.42e-02 1.65e+02 pdb=" CG TYR A 59 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR A 59 " -0.066 2.00e-02 2.50e+03 pdb=" CD2 TYR A 59 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 TYR A 59 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 59 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR A 59 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR A 59 " 0.104 2.00e-02 2.50e+03 pdb=" HD1 TYR A 59 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 TYR A 59 " -0.031 2.00e-02 2.50e+03 pdb=" HE1 TYR A 59 " 0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR A 59 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 32 " -0.139 2.00e-02 2.50e+03 6.39e-02 1.64e+02 pdb=" CG TRP B 32 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP B 32 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B 32 " -0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP B 32 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP B 32 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP B 32 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 32 " -0.055 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 32 " 0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP B 32 " -0.045 2.00e-02 2.50e+03 pdb=" HD1 TRP B 32 " 0.064 2.00e-02 2.50e+03 pdb=" HE1 TRP B 32 " 0.089 2.00e-02 2.50e+03 pdb=" HE3 TRP B 32 " 0.048 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 32 " -0.068 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 32 " 0.117 2.00e-02 2.50e+03 pdb=" HH2 TRP B 32 " -0.046 2.00e-02 2.50e+03 ... (remaining 1314 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 627 2.19 - 2.80: 15346 2.80 - 3.40: 23113 3.40 - 4.00: 29818 4.00 - 4.60: 43383 Nonbonded interactions: 112287 Sorted by model distance: nonbonded pdb=" H ILE B 29 " pdb=" H GLY B 30 " model vdw 1.593 2.100 nonbonded pdb=" HG SER B 185 " pdb=" OD2 ASP B 188 " model vdw 1.615 1.850 nonbonded pdb=" HG SER C 206 " pdb=" OD2 ASP C 209 " model vdw 1.629 1.850 nonbonded pdb=" HG SER B 31 " pdb=" OE1 GLU B 66 " model vdw 1.629 1.850 nonbonded pdb=" HG SER A 186 " pdb=" OE1 GLN B 163 " model vdw 1.654 1.850 ... (remaining 112282 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: 0.300 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: 0.140 Extract box with map and model: 1.470 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 32.410 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 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 : 0.013 0.047 4443 Z= 0.859 Angle : 1.974 10.053 6039 Z= 1.288 Chirality : 0.103 0.436 681 Planarity : 0.016 0.116 779 Dihedral : 14.418 88.513 1608 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 1.42 % Allowed : 9.56 % Favored : 89.03 % Rotamer: Outliers : 2.87 % Allowed : 3.69 % Favored : 93.44 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 16.67 % 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: -2.67 (0.32), residues: 565 helix: -1.12 (0.47), residues: 91 sheet: -0.78 (0.46), residues: 119 loop : -2.44 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.026 TRP A 36 HIS 0.017 0.004 HIS A 209 PHE 0.061 0.014 PHE B 212 TYR 0.182 0.034 TYR B 90 ARG 0.009 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 0.713 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8297 (p) cc_final: 0.8090 (m) REVERT: A 163 TRP cc_start: 0.6230 (m100) cc_final: 0.5555 (m100) REVERT: B 71 PHE cc_start: 0.6120 (t80) cc_final: 0.5349 (t80) REVERT: B 118 VAL cc_start: 0.8393 (t) cc_final: 0.8186 (p) REVERT: B 120 ILE cc_start: 0.3867 (mt) cc_final: 0.3626 (mt) outliers start: 14 outliers final: 8 residues processed: 147 average time/residue: 0.3661 time to fit residues: 66.1929 Evaluate side-chains 110 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 173 HIS B 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4443 Z= 0.275 Angle : 0.811 7.127 6039 Z= 0.438 Chirality : 0.047 0.244 681 Planarity : 0.006 0.044 779 Dihedral : 9.013 40.308 611 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.97 % Favored : 88.32 % Rotamer: Outliers : 0.20 % Allowed : 1.84 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -2.65 (0.34), residues: 565 helix: -0.21 (0.53), residues: 98 sheet: -1.40 (0.41), residues: 152 loop : -2.54 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 105 HIS 0.005 0.002 HIS A 173 PHE 0.013 0.002 PHE B 87 TYR 0.033 0.003 TYR B 90 ARG 0.004 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.719 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.6116 (m100) cc_final: 0.5214 (m100) REVERT: B 71 PHE cc_start: 0.6095 (t80) cc_final: 0.5536 (t80) REVERT: B 200 THR cc_start: 0.8771 (m) cc_final: 0.8458 (p) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.3964 time to fit residues: 52.9770 Evaluate side-chains 89 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4443 Z= 0.262 Angle : 0.742 6.636 6039 Z= 0.399 Chirality : 0.045 0.150 681 Planarity : 0.007 0.058 779 Dihedral : 8.091 38.407 611 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.69 % Favored : 84.96 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.85 (0.34), residues: 565 helix: 0.07 (0.51), residues: 98 sheet: -1.58 (0.40), residues: 154 loop : -2.82 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 186 HIS 0.006 0.002 HIS A 173 PHE 0.014 0.002 PHE B 71 TYR 0.032 0.003 TYR B 90 ARG 0.004 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.725 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: B 33 LEU cc_start: 0.7420 (pp) cc_final: 0.7186 (pp) REVERT: B 108 ASP cc_start: 0.7867 (t0) cc_final: 0.7394 (m-30) REVERT: B 200 THR cc_start: 0.8747 (m) cc_final: 0.8315 (p) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.4095 time to fit residues: 49.1444 Evaluate side-chains 84 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN B 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4443 Z= 0.190 Angle : 0.633 5.798 6039 Z= 0.340 Chirality : 0.042 0.134 681 Planarity : 0.006 0.046 779 Dihedral : 7.487 37.642 611 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.86 % Favored : 87.79 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.74 (0.34), residues: 565 helix: 0.45 (0.53), residues: 98 sheet: -1.58 (0.39), residues: 156 loop : -2.82 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 186 HIS 0.003 0.001 HIS A 173 PHE 0.044 0.002 PHE B 142 TYR 0.022 0.002 TYR B 90 ARG 0.003 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.694 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: symmetry clash REVERT: A 3 GLN cc_start: 0.7667 (mt0) cc_final: 0.7163 (mt0) REVERT: A 34 MET cc_start: 0.8154 (mtp) cc_final: 0.7897 (ppp) REVERT: B 108 ASP cc_start: 0.7549 (t0) cc_final: 0.7228 (m-30) REVERT: B 200 THR cc_start: 0.8706 (m) cc_final: 0.8377 (p) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.3426 time to fit residues: 41.5980 Evaluate side-chains 83 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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: 0.6313 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4443 Z= 0.248 Angle : 0.673 6.691 6039 Z= 0.362 Chirality : 0.044 0.138 681 Planarity : 0.006 0.050 779 Dihedral : 7.469 35.842 611 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.35 % Allowed : 15.75 % Favored : 83.89 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.96 (0.33), residues: 565 helix: 0.50 (0.53), residues: 98 sheet: -1.64 (0.40), residues: 148 loop : -3.08 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 36 HIS 0.004 0.001 HIS A 173 PHE 0.028 0.002 PHE B 142 TYR 0.028 0.003 TYR B 90 ARG 0.005 0.001 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.721 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: A 3 GLN cc_start: 0.7816 (mt0) cc_final: 0.7197 (mt0) REVERT: B 33 LEU cc_start: 0.7418 (pp) cc_final: 0.7177 (pp) REVERT: B 200 THR cc_start: 0.8759 (m) cc_final: 0.8403 (p) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3802 time to fit residues: 46.3381 Evaluate side-chains 78 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4443 Z= 0.220 Angle : 0.640 5.918 6039 Z= 0.342 Chirality : 0.043 0.135 681 Planarity : 0.006 0.048 779 Dihedral : 7.225 36.073 611 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.51 % Favored : 85.13 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.33), residues: 565 helix: 0.67 (0.53), residues: 98 sheet: -1.73 (0.39), residues: 155 loop : -3.16 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 36 HIS 0.004 0.001 HIS A 173 PHE 0.021 0.002 PHE B 142 TYR 0.028 0.003 TYR C 177 ARG 0.002 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.669 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: A 163 TRP cc_start: 0.6201 (m100) cc_final: 0.5708 (m100) REVERT: B 33 LEU cc_start: 0.7389 (pp) cc_final: 0.7091 (pp) REVERT: B 148 LYS cc_start: 0.7091 (tppt) cc_final: 0.6860 (tppt) REVERT: B 200 THR cc_start: 0.8852 (m) cc_final: 0.8503 (p) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.3578 time to fit residues: 42.5837 Evaluate side-chains 80 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4443 Z= 0.204 Angle : 0.624 5.774 6039 Z= 0.333 Chirality : 0.043 0.135 681 Planarity : 0.006 0.051 779 Dihedral : 7.040 35.900 611 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 15.04 % Favored : 84.60 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.99 (0.33), residues: 565 helix: 0.72 (0.53), residues: 98 sheet: -1.76 (0.39), residues: 154 loop : -3.15 (0.31), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 105 HIS 0.006 0.001 HIS A 173 PHE 0.015 0.002 PHE B 142 TYR 0.025 0.002 TYR B 195 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.636 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: A 163 TRP cc_start: 0.6225 (m100) cc_final: 0.5790 (m100) REVERT: B 33 LEU cc_start: 0.7345 (pp) cc_final: 0.7060 (pp) REVERT: B 108 ASP cc_start: 0.7598 (t0) cc_final: 0.6971 (m-30) REVERT: B 148 LYS cc_start: 0.6993 (tppt) cc_final: 0.6775 (tppt) REVERT: B 200 THR cc_start: 0.8849 (m) cc_final: 0.8478 (p) REVERT: C 200 THR cc_start: 0.8841 (p) cc_final: 0.8614 (t) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.3429 time to fit residues: 39.0694 Evaluate side-chains 80 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4443 Z= 0.160 Angle : 0.573 5.143 6039 Z= 0.303 Chirality : 0.042 0.144 681 Planarity : 0.006 0.051 779 Dihedral : 6.615 35.101 611 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.04 % Favored : 87.61 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.77 (0.34), residues: 565 helix: 0.95 (0.53), residues: 98 sheet: -1.74 (0.38), residues: 160 loop : -2.96 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 105 HIS 0.007 0.001 HIS A 173 PHE 0.017 0.001 PHE B 142 TYR 0.016 0.002 TYR B 195 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.683 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: A 163 TRP cc_start: 0.6158 (m100) cc_final: 0.5735 (m100) REVERT: B 33 LEU cc_start: 0.7206 (pp) cc_final: 0.6889 (pp) REVERT: B 108 ASP cc_start: 0.7504 (t0) cc_final: 0.6884 (m-30) REVERT: B 200 THR cc_start: 0.8730 (m) cc_final: 0.8409 (p) REVERT: C 200 THR cc_start: 0.8761 (p) cc_final: 0.8547 (t) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.3318 time to fit residues: 37.5792 Evaluate side-chains 77 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.0970 chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS B 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4443 Z= 0.151 Angle : 0.557 5.245 6039 Z= 0.294 Chirality : 0.041 0.137 681 Planarity : 0.005 0.051 779 Dihedral : 6.264 33.452 611 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.04 % Favored : 87.61 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.55 (0.34), residues: 565 helix: 1.19 (0.54), residues: 98 sheet: -1.63 (0.37), residues: 161 loop : -2.82 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 105 HIS 0.006 0.001 HIS A 173 PHE 0.014 0.001 PHE B 142 TYR 0.014 0.002 TYR B 195 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.725 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: A 34 MET cc_start: 0.8203 (mtp) cc_final: 0.7856 (ppp) REVERT: A 57 ASP cc_start: 0.7598 (m-30) cc_final: 0.7363 (m-30) REVERT: A 163 TRP cc_start: 0.6224 (m100) cc_final: 0.5817 (m100) REVERT: B 33 LEU cc_start: 0.7041 (pp) cc_final: 0.6787 (pp) REVERT: B 108 ASP cc_start: 0.7636 (t0) cc_final: 0.6712 (m-30) REVERT: B 200 THR cc_start: 0.8693 (m) cc_final: 0.8405 (p) REVERT: C 139 THR cc_start: 0.7122 (m) cc_final: 0.6915 (m) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.3063 time to fit residues: 36.8970 Evaluate side-chains 81 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4443 Z= 0.224 Angle : 0.620 5.603 6039 Z= 0.329 Chirality : 0.043 0.138 681 Planarity : 0.007 0.095 779 Dihedral : 6.623 34.802 611 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.51 % Favored : 85.13 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.71 (0.34), residues: 565 helix: 1.26 (0.54), residues: 96 sheet: -1.71 (0.38), residues: 156 loop : -2.97 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 186 HIS 0.007 0.002 HIS A 173 PHE 0.009 0.001 PHE B 71 TYR 0.026 0.002 TYR B 90 ARG 0.004 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.751 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: A 34 MET cc_start: 0.8290 (mtp) cc_final: 0.7811 (ppp) REVERT: A 163 TRP cc_start: 0.6330 (m100) cc_final: 0.6009 (m100) REVERT: B 33 LEU cc_start: 0.7220 (pp) cc_final: 0.6896 (pp) REVERT: B 200 THR cc_start: 0.8749 (m) cc_final: 0.8410 (p) REVERT: C 139 THR cc_start: 0.7088 (m) cc_final: 0.6857 (m) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.3621 time to fit residues: 41.3518 Evaluate side-chains 81 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.0050 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 0.0970 chunk 50 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.222805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.192956 restraints weight = 14841.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.198304 restraints weight = 9724.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.201574 restraints weight = 7046.098| |-----------------------------------------------------------------------------| r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.6204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4443 Z= 0.151 Angle : 0.555 4.756 6039 Z= 0.292 Chirality : 0.041 0.137 681 Planarity : 0.006 0.085 779 Dihedral : 6.193 33.924 611 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.44 % Favored : 89.20 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.58 (0.34), residues: 565 helix: 1.38 (0.55), residues: 98 sheet: -1.76 (0.36), residues: 163 loop : -2.84 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 186 HIS 0.006 0.001 HIS A 173 PHE 0.011 0.001 PHE B 142 TYR 0.017 0.002 TYR B 90 ARG 0.003 0.000 ARG B 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2583.08 seconds wall clock time: 46 minutes 26.12 seconds (2786.12 seconds total)