Starting phenix.real_space_refine on Wed Feb 14 04:52:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/02_2024/8crb_16807.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/02_2024/8crb_16807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/02_2024/8crb_16807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/02_2024/8crb_16807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/02_2024/8crb_16807.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/02_2024/8crb_16807.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 13 5.16 5 C 2743 2.51 5 N 738 2.21 5 O 885 1.98 5 H 4286 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 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 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 122": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 222": "OD1" <-> "OD2" Residue "A ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 17": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 193": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 128": "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 PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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-5238/modules/chem_data/mon_lib" Total number of atoms: 8665 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3320 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Chain: "B" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3187 Classifications: {'peptide': 216} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 198} Chain: "C" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2158 Classifications: {'peptide': 139} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131} Time building chain proxies: 5.64, per 1000 atoms: 0.65 Number of scatterers: 8665 At special positions: 0 Unit cell: (73.1, 81.6, 113.9, 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 13 16.00 O 885 8.00 N 738 7.00 C 2743 6.00 H 4286 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: 7.12 Conformation dependent library (CDL) restraints added in 845.7 milliseconds 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1064 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 11 sheets defined 21.8% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.666A pdb=" N ASP A 90 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 4.321A pdb=" N SER A 146 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'C' and resid 129 through 158 removed outlier: 3.584A pdb=" N ALA C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 189 through 198 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 236 through 264 Proline residue: C 250 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.546A pdb=" N THR A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.546A pdb=" N THR A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 116 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 137 removed outlier: 3.518A pdb=" N SER A 134 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 168 Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.715A pdb=" N ASP B 86 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 39 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA8, first strand: chain 'B' and resid 118 through 122 removed outlier: 6.162A pdb=" N TYR B 176 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 118 through 122 removed outlier: 6.162A pdb=" N TYR B 176 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 163 198 hydrogen bonds defined for protein. 501 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: 2.96 Time building geometry restraints manager: 7.38 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: 4275 1.11 - 1.29: 732 1.29 - 1.46: 1380 1.46 - 1.64: 2361 1.64 - 1.81: 15 Bond restraints: 8763 Sorted by residual: bond pdb=" N SER A 49 " pdb=" H SER A 49 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N ASN A 74 " pdb=" H ASN A 74 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N GLY B 69 " pdb=" H GLY B 69 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N ASN B 174 " pdb=" H ASN B 174 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CD1 PHE A 160 " pdb=" HD1 PHE A 160 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 8758 not shown) Histogram of bond angle deviations from ideal: 93.61 - 102.04: 27 102.04 - 110.47: 8333 110.47 - 118.89: 4046 118.89 - 127.32: 3340 127.32 - 135.75: 68 Bond angle restraints: 15814 Sorted by residual: angle pdb=" N PRO B 7 " pdb=" CA PRO B 7 " pdb=" C PRO B 7 " ideal model delta sigma weight residual 110.70 121.25 -10.55 1.22e+00 6.72e-01 7.48e+01 angle pdb=" C LYS B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta sigma weight residual 120.50 128.86 -8.36 1.34e+00 5.57e-01 3.89e+01 angle pdb=" CA PHE A 114 " pdb=" CB PHE A 114 " pdb=" CG PHE A 114 " ideal model delta sigma weight residual 113.80 119.77 -5.97 1.00e+00 1.00e+00 3.57e+01 angle pdb=" CA PHE A 27 " pdb=" CB PHE A 27 " pdb=" CG PHE A 27 " ideal model delta sigma weight residual 113.80 119.39 -5.59 1.00e+00 1.00e+00 3.13e+01 angle pdb=" C GLY B 102 " pdb=" N PRO B 103 " pdb=" CA PRO B 103 " ideal model delta sigma weight residual 119.87 125.68 -5.81 1.04e+00 9.25e-01 3.12e+01 ... (remaining 15809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 3783 17.77 - 35.55: 282 35.55 - 53.32: 102 53.32 - 71.10: 30 71.10 - 88.87: 8 Dihedral angle restraints: 4205 sinusoidal: 2281 harmonic: 1924 Sorted by residual: dihedral pdb=" CA PRO B 7 " pdb=" C PRO B 7 " pdb=" N PRO B 8 " pdb=" CA PRO B 8 " ideal model delta harmonic sigma weight residual -180.00 -150.74 -29.26 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA SER B 2 " pdb=" C SER B 2 " pdb=" N VAL B 3 " pdb=" CA VAL B 3 " ideal model delta harmonic sigma weight residual -180.00 -150.96 -29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ASN C 234 " pdb=" C ASN C 234 " pdb=" N ASN C 235 " pdb=" CA ASN C 235 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 4202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 384 0.083 - 0.165: 226 0.165 - 0.248: 59 0.248 - 0.330: 11 0.330 - 0.412: 2 Chirality restraints: 682 Sorted by residual: chirality pdb=" CA ASN B 174 " pdb=" N ASN B 174 " pdb=" C ASN B 174 " pdb=" CB ASN B 174 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CA TYR A 108 " pdb=" N TYR A 108 " pdb=" C TYR A 108 " pdb=" CB TYR A 108 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA ASN A 218 " pdb=" N ASN A 218 " pdb=" C ASN A 218 " pdb=" CB ASN A 218 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 679 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 37 " 0.307 2.00e-02 2.50e+03 1.40e-01 5.87e+02 pdb=" CG TYR B 37 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 37 " -0.086 2.00e-02 2.50e+03 pdb=" CD2 TYR B 37 " -0.094 2.00e-02 2.50e+03 pdb=" CE1 TYR B 37 " -0.082 2.00e-02 2.50e+03 pdb=" CE2 TYR B 37 " -0.074 2.00e-02 2.50e+03 pdb=" CZ TYR B 37 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 37 " 0.306 2.00e-02 2.50e+03 pdb=" HD1 TYR B 37 " -0.047 2.00e-02 2.50e+03 pdb=" HD2 TYR B 37 " -0.073 2.00e-02 2.50e+03 pdb=" HE1 TYR B 37 " -0.077 2.00e-02 2.50e+03 pdb=" HE2 TYR B 37 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 117 " 0.179 2.00e-02 2.50e+03 1.18e-01 5.53e+02 pdb=" CG TRP A 117 " 0.094 2.00e-02 2.50e+03 pdb=" CD1 TRP A 117 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TRP A 117 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP A 117 " -0.092 2.00e-02 2.50e+03 pdb=" CE2 TRP A 117 " -0.078 2.00e-02 2.50e+03 pdb=" CE3 TRP A 117 " -0.133 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 117 " -0.037 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 117 " -0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP A 117 " 0.078 2.00e-02 2.50e+03 pdb=" HD1 TRP A 117 " 0.101 2.00e-02 2.50e+03 pdb=" HE1 TRP A 117 " -0.153 2.00e-02 2.50e+03 pdb=" HE3 TRP A 117 " -0.188 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 117 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 117 " 0.005 2.00e-02 2.50e+03 pdb=" HH2 TRP A 117 " 0.254 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 36 " -0.175 2.00e-02 2.50e+03 7.09e-02 2.01e+02 pdb=" CG TRP A 36 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP A 36 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 36 " 0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP A 36 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 TRP A 36 " 0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP A 36 " 0.069 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 36 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 36 " 0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP A 36 " -0.037 2.00e-02 2.50e+03 pdb=" HD1 TRP A 36 " -0.047 2.00e-02 2.50e+03 pdb=" HE1 TRP A 36 " 0.106 2.00e-02 2.50e+03 pdb=" HE3 TRP A 36 " 0.079 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 36 " -0.076 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 36 " 0.021 2.00e-02 2.50e+03 pdb=" HH2 TRP A 36 " -0.090 2.00e-02 2.50e+03 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 639 2.19 - 2.79: 15350 2.79 - 3.39: 23731 3.39 - 4.00: 29777 4.00 - 4.60: 43550 Nonbonded interactions: 113047 Sorted by model distance: nonbonded pdb=" OD1 ASP A 73 " pdb=" HG SER A 75 " model vdw 1.584 1.850 nonbonded pdb=" H ASP A 73 " pdb=" HG LEU A 79 " model vdw 1.586 2.270 nonbonded pdb=" OD2 ASP C 199 " pdb=" HG SER C 214 " model vdw 1.601 1.850 nonbonded pdb=" OD1 ASP C 173 " pdb=" HG1 THR C 175 " model vdw 1.622 1.850 nonbonded pdb=" HG SER A 54 " pdb=" OD2 ASP C 246 " model vdw 1.625 1.850 ... (remaining 113042 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: 0.130 Extract box with map and model: 1.490 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 32.320 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 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 0.043 4477 Z= 0.858 Angle : 1.985 10.554 6092 Z= 1.299 Chirality : 0.105 0.412 682 Planarity : 0.016 0.162 789 Dihedral : 14.753 88.871 1621 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 1.91 % Allowed : 10.07 % Favored : 88.02 % Rotamer: Outliers : 1.23 % Allowed : 5.33 % Favored : 93.44 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 11.11 % 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: -2.65 (0.30), residues: 576 helix: -1.56 (0.40), residues: 109 sheet: -1.03 (0.52), residues: 98 loop : -2.13 (0.28), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.144 0.030 TRP A 117 HIS 0.013 0.007 HIS A 214 PHE 0.079 0.017 PHE A 114 TYR 0.279 0.029 TYR B 37 ARG 0.004 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 0.629 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: 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: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.0319 (p90) cc_final: -0.0730 (p90) REVERT: A 67 ARG cc_start: 0.7665 (mtt180) cc_final: 0.7382 (mpp80) REVERT: A 117 TRP cc_start: 0.7366 (m100) cc_final: 0.7067 (m100) REVERT: A 225 VAL cc_start: 0.7751 (t) cc_final: 0.7332 (t) REVERT: B 67 LYS cc_start: 0.7176 (pttt) cc_final: 0.6547 (ptpp) REVERT: B 159 VAL cc_start: 0.6504 (m) cc_final: 0.6280 (t) REVERT: B 180 SER cc_start: 0.8146 (p) cc_final: 0.7789 (t) REVERT: C 139 THR cc_start: 0.8712 (m) cc_final: 0.8502 (p) REVERT: C 143 LYS cc_start: 0.8901 (tttt) cc_final: 0.8693 (tttt) REVERT: C 153 ASN cc_start: 0.8141 (m-40) cc_final: 0.7856 (m-40) outliers start: 6 outliers final: 3 residues processed: 150 average time/residue: 0.4772 time to fit residues: 84.1440 Evaluate side-chains 105 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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: 6.9990 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN B 174 ASN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 4477 Z= 0.358 Angle : 0.891 6.533 6092 Z= 0.499 Chirality : 0.046 0.183 682 Planarity : 0.007 0.078 789 Dihedral : 8.711 32.272 630 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.81 % Favored : 87.67 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -2.78 (0.31), residues: 576 helix: -0.68 (0.44), residues: 107 sheet: -1.42 (0.39), residues: 150 loop : -2.56 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 47 HIS 0.003 0.002 HIS A 178 PHE 0.020 0.003 PHE A 29 TYR 0.035 0.003 TYR B 37 ARG 0.004 0.001 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.729 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.7118 (m100) cc_final: 0.6893 (m100) REVERT: A 124 THR cc_start: 0.7231 (m) cc_final: 0.6209 (m) REVERT: B 67 LYS cc_start: 0.7155 (pttt) cc_final: 0.6544 (ptpp) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.4055 time to fit residues: 58.1677 Evaluate side-chains 86 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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: 0.9990 chunk 15 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 234 ASN C 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4477 Z= 0.266 Angle : 0.750 6.074 6092 Z= 0.418 Chirality : 0.045 0.181 682 Planarity : 0.007 0.067 789 Dihedral : 7.692 31.535 630 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.02 % Favored : 86.98 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.88 (0.32), residues: 576 helix: -0.32 (0.46), residues: 107 sheet: -1.66 (0.39), residues: 156 loop : -2.71 (0.31), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 47 HIS 0.004 0.001 HIS A 178 PHE 0.020 0.002 PHE A 68 TYR 0.022 0.002 TYR B 37 ARG 0.003 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.700 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.7074 (mmtt) cc_final: 0.5930 (mttt) REVERT: A 115 GLU cc_start: 0.6598 (tm-30) cc_final: 0.6239 (tm-30) REVERT: B 67 LYS cc_start: 0.7150 (pttt) cc_final: 0.6491 (ptpp) REVERT: B 137 VAL cc_start: 0.7555 (t) cc_final: 0.7342 (t) REVERT: C 217 GLN cc_start: 0.6750 (mt0) cc_final: 0.6363 (mt0) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3867 time to fit residues: 52.4055 Evaluate side-chains 92 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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: 6.9990 chunk 5 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 0.0870 chunk 51 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4477 Z= 0.194 Angle : 0.666 5.658 6092 Z= 0.364 Chirality : 0.044 0.165 682 Planarity : 0.006 0.070 789 Dihedral : 6.985 32.012 630 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.42 % Favored : 89.24 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.32), residues: 576 helix: 0.10 (0.46), residues: 108 sheet: -1.51 (0.41), residues: 149 loop : -2.51 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 47 HIS 0.003 0.001 HIS A 178 PHE 0.017 0.002 PHE A 68 TYR 0.025 0.002 TYR A 60 ARG 0.004 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 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: 0 poor density : 109 time to evaluate : 0.744 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8557 (mpt180) cc_final: 0.7881 (mpp-170) REVERT: B 67 LYS cc_start: 0.7038 (pttt) cc_final: 0.6339 (ptpp) REVERT: B 112 GLN cc_start: 0.8761 (tt0) cc_final: 0.8468 (tm-30) REVERT: B 137 VAL cc_start: 0.7671 (t) cc_final: 0.7423 (t) REVERT: C 141 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8872 (mt-10) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3617 time to fit residues: 49.0271 Evaluate side-chains 90 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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: 8.9990 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4477 Z= 0.262 Angle : 0.692 5.411 6092 Z= 0.381 Chirality : 0.043 0.165 682 Planarity : 0.007 0.070 789 Dihedral : 7.074 32.236 630 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.02 % Favored : 86.81 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.33), residues: 576 helix: 0.36 (0.48), residues: 102 sheet: -1.76 (0.40), residues: 152 loop : -2.47 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 47 HIS 0.003 0.001 HIS A 178 PHE 0.023 0.002 PHE A 180 TYR 0.020 0.002 TYR B 37 ARG 0.006 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 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 : 0.758 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: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8692 (mpt180) cc_final: 0.8058 (mpp-170) REVERT: B 67 LYS cc_start: 0.7041 (pttt) cc_final: 0.6285 (ptpp) REVERT: B 137 VAL cc_start: 0.7618 (t) cc_final: 0.7414 (t) REVERT: C 217 GLN cc_start: 0.6798 (mt0) cc_final: 0.6385 (mt0) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3748 time to fit residues: 45.4234 Evaluate side-chains 87 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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: 4.9990 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 GLN B 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4477 Z= 0.206 Angle : 0.641 5.129 6092 Z= 0.350 Chirality : 0.043 0.160 682 Planarity : 0.006 0.069 789 Dihedral : 6.753 31.730 630 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.15 % Favored : 87.67 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.45 (0.34), residues: 576 helix: 0.59 (0.48), residues: 102 sheet: -1.75 (0.41), residues: 150 loop : -2.38 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 36 HIS 0.003 0.001 HIS A 214 PHE 0.024 0.002 PHE A 68 TYR 0.014 0.002 TYR B 37 ARG 0.005 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8719 (mpt180) cc_final: 0.8139 (mpp-170) REVERT: B 67 LYS cc_start: 0.7072 (pttt) cc_final: 0.6266 (ptpp) REVERT: B 135 THR cc_start: 0.7013 (m) cc_final: 0.6759 (m) REVERT: B 137 VAL cc_start: 0.7627 (t) cc_final: 0.7364 (t) REVERT: B 174 ASN cc_start: 0.7722 (m-40) cc_final: 0.7385 (t0) REVERT: C 217 GLN cc_start: 0.6914 (mt0) cc_final: 0.6507 (mt0) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3520 time to fit residues: 45.3756 Evaluate side-chains 93 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.6374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4477 Z= 0.221 Angle : 0.640 5.082 6092 Z= 0.350 Chirality : 0.042 0.158 682 Planarity : 0.007 0.071 789 Dihedral : 6.669 27.816 630 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.85 % Favored : 86.81 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.37 (0.34), residues: 576 helix: 0.65 (0.49), residues: 102 sheet: -1.65 (0.42), residues: 152 loop : -2.36 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 36 HIS 0.002 0.001 HIS A 178 PHE 0.018 0.002 PHE B 101 TYR 0.017 0.002 TYR B 37 ARG 0.004 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.769 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: symmetry clash REVERT: A 67 ARG cc_start: 0.8596 (mpt180) cc_final: 0.8025 (mpp-170) REVERT: B 67 LYS cc_start: 0.7097 (pttt) cc_final: 0.6247 (ptpp) REVERT: B 135 THR cc_start: 0.7002 (m) cc_final: 0.6767 (m) REVERT: B 137 VAL cc_start: 0.7637 (t) cc_final: 0.7420 (t) REVERT: B 174 ASN cc_start: 0.7719 (m-40) cc_final: 0.7414 (t0) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3526 time to fit residues: 46.7204 Evaluate side-chains 90 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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: 5.9990 chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4477 Z= 0.297 Angle : 0.704 5.395 6092 Z= 0.387 Chirality : 0.044 0.163 682 Planarity : 0.007 0.071 789 Dihedral : 7.038 26.448 630 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.52 % Allowed : 15.45 % Favored : 84.03 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.33), residues: 576 helix: 0.37 (0.49), residues: 99 sheet: -2.04 (0.43), residues: 134 loop : -2.41 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 36 HIS 0.004 0.002 HIS B 201 PHE 0.016 0.002 PHE A 114 TYR 0.015 0.002 TYR B 99 ARG 0.006 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.749 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8316 (mpt180) cc_final: 0.7840 (mpp-170) REVERT: B 67 LYS cc_start: 0.7162 (pttt) cc_final: 0.6259 (ptpp) REVERT: B 135 THR cc_start: 0.7152 (m) cc_final: 0.6902 (m) REVERT: B 137 VAL cc_start: 0.7692 (t) cc_final: 0.7451 (t) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.3875 time to fit residues: 45.4547 Evaluate side-chains 86 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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: 6.9990 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.6669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4477 Z= 0.166 Angle : 0.604 5.260 6092 Z= 0.324 Chirality : 0.043 0.151 682 Planarity : 0.006 0.072 789 Dihedral : 6.111 24.426 630 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.94 % Favored : 88.54 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.14 (0.35), residues: 576 helix: 0.78 (0.50), residues: 99 sheet: -1.38 (0.43), residues: 145 loop : -2.21 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 36 HIS 0.004 0.001 HIS A 214 PHE 0.008 0.001 PHE A 29 TYR 0.012 0.001 TYR B 37 ARG 0.003 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.839 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8236 (mpt180) cc_final: 0.7748 (mpp-170) REVERT: B 67 LYS cc_start: 0.7018 (pttt) cc_final: 0.6329 (ptpp) REVERT: B 135 THR cc_start: 0.6970 (m) cc_final: 0.6741 (m) REVERT: B 137 VAL cc_start: 0.7820 (t) cc_final: 0.7588 (t) REVERT: C 141 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8896 (mt-10) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3789 time to fit residues: 48.7358 Evaluate side-chains 89 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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: 7.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.6852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4477 Z= 0.170 Angle : 0.594 5.335 6092 Z= 0.321 Chirality : 0.042 0.147 682 Planarity : 0.006 0.071 789 Dihedral : 5.906 23.311 630 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.33 % Favored : 87.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.35), residues: 576 helix: 1.02 (0.51), residues: 98 sheet: -1.46 (0.44), residues: 137 loop : -2.16 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 36 HIS 0.003 0.001 HIS A 214 PHE 0.008 0.001 PHE A 114 TYR 0.012 0.001 TYR B 99 ARG 0.004 0.000 ARG A 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 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: 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 67 ARG cc_start: 0.8307 (mpt180) cc_final: 0.7803 (mpp-170) REVERT: B 67 LYS cc_start: 0.6959 (pttt) cc_final: 0.6265 (ptpp) REVERT: B 135 THR cc_start: 0.6893 (m) cc_final: 0.6655 (m) REVERT: B 137 VAL cc_start: 0.7832 (t) cc_final: 0.7600 (t) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3676 time to fit residues: 47.0689 Evaluate side-chains 89 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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: 5.9990 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.126896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.105311 restraints weight = 47027.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.109924 restraints weight = 28719.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.113212 restraints weight = 19368.062| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.6894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4477 Z= 0.286 Angle : 0.676 5.196 6092 Z= 0.370 Chirality : 0.043 0.172 682 Planarity : 0.007 0.068 789 Dihedral : 6.466 23.220 630 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.76 % Favored : 84.72 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.42 (0.34), residues: 576 helix: 0.77 (0.50), residues: 98 sheet: -1.66 (0.41), residues: 151 loop : -2.42 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 36 HIS 0.003 0.002 HIS A 178 PHE 0.015 0.002 PHE A 114 TYR 0.016 0.002 TYR A 159 ARG 0.006 0.001 ARG A 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2495.93 seconds wall clock time: 45 minutes 1.12 seconds (2701.12 seconds total)