Starting phenix.real_space_refine on Mon Mar 11 02:56:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spb_40678/03_2024/8spb_40678.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spb_40678/03_2024/8spb_40678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spb_40678/03_2024/8spb_40678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spb_40678/03_2024/8spb_40678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spb_40678/03_2024/8spb_40678.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spb_40678/03_2024/8spb_40678.pdb" } resolution = 3.2 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= 0.065 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 4264 2.51 5 N 1134 2.21 5 O 1278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 223": "OE1" <-> "OE2" Residue "A ASP 227": "OD1" <-> "OD2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "a GLU 123": "OE1" <-> "OE2" Residue "a GLU 124": "OE1" <-> "OE2" Residue "a TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 164": "OE1" <-> "OE2" Residue "a GLU 167": "OE1" <-> "OE2" Residue "a GLU 177": "OE1" <-> "OE2" Residue "a GLU 214": "OE1" <-> "OE2" Residue "a GLU 223": "OE1" <-> "OE2" Residue "c PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 34": "OE1" <-> "OE2" Residue "c PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 164": "OE1" <-> "OE2" Residue "c GLU 166": "OE1" <-> "OE2" Residue "c PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6726 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1332 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain: "B" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 731 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "C" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1300 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 4, 'TRANS': 155} Chain breaks: 1 Chain: "a" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1332 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain: "b" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 731 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "c" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1300 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 4, 'TRANS': 155} Chain breaks: 1 Time building chain proxies: 4.01, per 1000 atoms: 0.60 Number of scatterers: 6726 At special positions: 0 Unit cell: (72.21, 138.61, 78.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1278 8.00 N 1134 7.00 C 4264 6.00 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: 2.64 Conformation dependent library (CDL) restraints added in 1.4 seconds 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1596 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 16 sheets defined 22.2% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 110 through 119 removed outlier: 3.885A pdb=" N PHE A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 115 " --> pdb=" O HIS A 111 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 169 Processing helix chain 'A' and resid 180 through 193 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.597A pdb=" N PHE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.872A pdb=" N LYS A 247 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 334 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'a' and resid 110 through 121 removed outlier: 3.520A pdb=" N CYS a 118 " --> pdb=" O PHE a 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS a 119 " --> pdb=" O LEU a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 154 through 169 Processing helix chain 'a' and resid 180 through 193 Processing helix chain 'a' and resid 194 through 200 removed outlier: 3.522A pdb=" N LYS a 198 " --> pdb=" O PRO a 195 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 238 Processing helix chain 'a' and resid 243 through 247 Processing helix chain 'b' and resid 321 through 334 Processing helix chain 'b' and resid 338 through 350 Processing helix chain 'c' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.792A pdb=" N ALA A 138 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 204 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THR A 203 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE A 254 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU A 205 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLN A 256 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A 207 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 217 Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 269 Processing sheet with id=AA4, first strand: chain 'B' and resid 291 through 294 Processing sheet with id=AA5, first strand: chain 'B' and resid 319 through 320 Processing sheet with id=AA6, first strand: chain 'C' and resid 24 through 25 removed outlier: 3.697A pdb=" N ALA C 162 " --> pdb=" O ILE C 173 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.526A pdb=" N SER C 46 " --> pdb=" O MET C 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 88 removed outlier: 5.954A pdb=" N ILE C 100 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 85 through 88 removed outlier: 3.603A pdb=" N MET C 149 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 172 through 176 removed outlier: 3.832A pdb=" N ALA a 138 " --> pdb=" O SER a 172 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU a 137 " --> pdb=" O PHE a 204 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL a 206 " --> pdb=" O LEU a 137 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU a 139 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N MET a 208 " --> pdb=" O LEU a 139 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE a 141 " --> pdb=" O MET a 208 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE b 301 " --> pdb=" O LYS a 251 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 215 through 217 Processing sheet with id=AB3, first strand: chain 'b' and resid 319 through 320 Processing sheet with id=AB4, first strand: chain 'c' and resid 18 through 19 removed outlier: 6.153A pdb=" N LEU c 23 " --> pdb=" O LEU c 172 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU c 172 " --> pdb=" O LEU c 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE c 25 " --> pdb=" O PHE c 170 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA c 162 " --> pdb=" O ILE c 173 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 45 through 46 removed outlier: 3.508A pdb=" N SER c 46 " --> pdb=" O MET c 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'c' and resid 84 through 88 removed outlier: 6.122A pdb=" N ILE c 100 " --> pdb=" O LEU c 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 84 through 88 removed outlier: 3.918A pdb=" N MET c 149 " --> pdb=" O VAL c 189 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL c 189 " --> pdb=" O MET c 149 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 561 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: 1.73 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2190 1.34 - 1.46: 942 1.46 - 1.57: 3650 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6856 Sorted by residual: bond pdb=" N ILE C 11 " pdb=" CA ILE C 11 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N LYS a 249 " pdb=" CA LYS a 249 " ideal model delta sigma weight residual 1.453 1.487 -0.035 1.18e-02 7.18e+03 8.67e+00 bond pdb=" N LYS c 148 " pdb=" CA LYS c 148 " ideal model delta sigma weight residual 1.454 1.485 -0.032 1.18e-02 7.18e+03 7.21e+00 bond pdb=" N LYS C 148 " pdb=" CA LYS C 148 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 7.15e+00 bond pdb=" N ILE a 140 " pdb=" CA ILE a 140 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.28e-02 6.10e+03 6.49e+00 ... (remaining 6851 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.10: 144 106.10 - 113.07: 3600 113.07 - 120.04: 2394 120.04 - 127.01: 3042 127.01 - 133.98: 50 Bond angle restraints: 9230 Sorted by residual: angle pdb=" N ASN C 12 " pdb=" CA ASN C 12 " pdb=" C ASN C 12 " ideal model delta sigma weight residual 108.17 124.31 -16.14 1.85e+00 2.92e-01 7.61e+01 angle pdb=" N ASN C 12 " pdb=" CA ASN C 12 " pdb=" CB ASN C 12 " ideal model delta sigma weight residual 110.46 101.21 9.25 1.42e+00 4.96e-01 4.24e+01 angle pdb=" N ILE C 11 " pdb=" CA ILE C 11 " pdb=" C ILE C 11 " ideal model delta sigma weight residual 109.34 122.27 -12.93 2.08e+00 2.31e-01 3.86e+01 angle pdb=" C ARG C 167 " pdb=" CA ARG C 167 " pdb=" CB ARG C 167 " ideal model delta sigma weight residual 117.23 110.34 6.89 1.36e+00 5.41e-01 2.57e+01 angle pdb=" C ARG c 167 " pdb=" CA ARG c 167 " pdb=" CB ARG c 167 " ideal model delta sigma weight residual 117.23 110.39 6.84 1.36e+00 5.41e-01 2.53e+01 ... (remaining 9225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3573 17.99 - 35.97: 465 35.97 - 53.96: 132 53.96 - 71.94: 17 71.94 - 89.93: 9 Dihedral angle restraints: 4196 sinusoidal: 1756 harmonic: 2440 Sorted by residual: dihedral pdb=" CA VAL c 47 " pdb=" C VAL c 47 " pdb=" N ILE c 48 " pdb=" CA ILE c 48 " ideal model delta harmonic sigma weight residual -180.00 -158.96 -21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA VAL C 47 " pdb=" C VAL C 47 " pdb=" N ILE C 48 " pdb=" CA ILE C 48 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA TYR c 37 " pdb=" C TYR c 37 " pdb=" N PHE c 38 " pdb=" CA PHE c 38 " ideal model delta harmonic sigma weight residual -180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 4193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 818 0.055 - 0.109: 162 0.109 - 0.164: 30 0.164 - 0.218: 3 0.218 - 0.273: 3 Chirality restraints: 1016 Sorted by residual: chirality pdb=" CA ASN C 12 " pdb=" N ASN C 12 " pdb=" C ASN C 12 " pdb=" CB ASN C 12 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA THR c 188 " pdb=" N THR c 188 " pdb=" C THR c 188 " pdb=" CB THR c 188 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ILE C 11 " pdb=" N ILE C 11 " pdb=" C ILE C 11 " pdb=" CB ILE C 11 " both_signs ideal model delta sigma weight residual False 2.43 2.21 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1013 not shown) Planarity restraints: 1192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR b 307 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO b 308 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO b 308 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO b 308 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 124 " 0.041 5.00e-02 4.00e+02 6.16e-02 6.08e+00 pdb=" N PRO C 125 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR c 37 " 0.007 2.00e-02 2.50e+03 1.20e-02 2.88e+00 pdb=" CG TYR c 37 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR c 37 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR c 37 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR c 37 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR c 37 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR c 37 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR c 37 " 0.000 2.00e-02 2.50e+03 ... (remaining 1189 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 985 2.76 - 3.30: 6429 3.30 - 3.83: 10700 3.83 - 4.37: 12308 4.37 - 4.90: 21335 Nonbonded interactions: 51757 Sorted by model distance: nonbonded pdb=" N GLU C 31 " pdb=" OE1 GLU C 31 " model vdw 2.227 2.520 nonbonded pdb=" OG SER c 86 " pdb=" OG1 THR c 99 " model vdw 2.237 2.440 nonbonded pdb=" OG SER C 86 " pdb=" OG1 THR C 99 " model vdw 2.261 2.440 nonbonded pdb=" O THR A 135 " pdb=" OG1 THR A 135 " model vdw 2.268 2.440 nonbonded pdb=" O PHE B 330 " pdb=" OG SER B 334 " model vdw 2.278 2.440 ... (remaining 51752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } 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 individual isotropic 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: 0.980 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: 0.010 Extract box with map and model: 4.590 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.720 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 : 0.003 0.044 6856 Z= 0.207 Angle : 0.731 16.137 9230 Z= 0.430 Chirality : 0.047 0.273 1016 Planarity : 0.004 0.066 1192 Dihedral : 17.299 89.931 2600 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.18 % Allowed : 25.79 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.28), residues: 812 helix: 0.53 (0.41), residues: 148 sheet: -0.38 (0.42), residues: 160 loop : -1.61 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 PHE 0.017 0.001 PHE c 170 TYR 0.028 0.001 TYR c 37 ARG 0.003 0.000 ARG c 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 238 time to evaluate : 0.951 Fit side-chains REVERT: C 138 PHE cc_start: 0.6988 (m-80) cc_final: 0.6609 (m-80) REVERT: C 152 GLU cc_start: 0.3870 (tp30) cc_final: 0.3668 (tp30) REVERT: a 182 ARG cc_start: 0.8132 (mmp80) cc_final: 0.7921 (mmt180) REVERT: c 103 LYS cc_start: 0.5659 (tttt) cc_final: 0.5165 (tttp) outliers start: 9 outliers final: 4 residues processed: 244 average time/residue: 0.2004 time to fit residues: 62.9018 Evaluate side-chains 218 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain b residue 341 GLU Chi-restraints excluded: chain c residue 119 PHE Chi-restraints excluded: chain c residue 160 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.0270 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN C 12 ASN ** a 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6856 Z= 0.208 Angle : 0.550 7.390 9230 Z= 0.295 Chirality : 0.042 0.148 1016 Planarity : 0.004 0.041 1192 Dihedral : 5.973 59.130 899 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.74 % Allowed : 26.58 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.28), residues: 812 helix: 0.96 (0.40), residues: 152 sheet: -0.07 (0.43), residues: 160 loop : -1.58 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 PHE 0.021 0.001 PHE C 13 TYR 0.018 0.001 TYR c 37 ARG 0.002 0.000 ARG a 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 216 time to evaluate : 0.793 Fit side-chains REVERT: B 373 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7948 (mm) REVERT: C 96 MET cc_start: 0.4601 (OUTLIER) cc_final: 0.4381 (mtp) REVERT: a 214 GLU cc_start: 0.7431 (mp0) cc_final: 0.7224 (mp0) REVERT: c 96 MET cc_start: 0.4527 (OUTLIER) cc_final: 0.4194 (mtm) REVERT: c 152 GLU cc_start: 0.4164 (tp30) cc_final: 0.3962 (tp30) outliers start: 36 outliers final: 18 residues processed: 231 average time/residue: 0.1904 time to fit residues: 57.4727 Evaluate side-chains 224 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain a residue 143 ASN Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 341 GLU Chi-restraints excluded: chain b residue 342 VAL Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain c residue 96 MET Chi-restraints excluded: chain c residue 104 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 6856 Z= 0.382 Angle : 0.629 8.417 9230 Z= 0.335 Chirality : 0.044 0.139 1016 Planarity : 0.004 0.041 1192 Dihedral : 5.569 50.965 895 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 7.37 % Allowed : 24.61 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.28), residues: 812 helix: 0.49 (0.39), residues: 154 sheet: -0.39 (0.42), residues: 164 loop : -1.71 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP b 335 HIS 0.004 0.001 HIS A 221 PHE 0.017 0.002 PHE C 13 TYR 0.018 0.002 TYR c 37 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 220 time to evaluate : 0.792 Fit side-chains REVERT: A 170 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.7086 (m-30) REVERT: B 373 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8056 (mm) REVERT: C 123 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7881 (m110) REVERT: C 138 PHE cc_start: 0.7550 (m-80) cc_final: 0.7310 (m-80) REVERT: C 191 ASN cc_start: 0.8170 (t0) cc_final: 0.7965 (t0) REVERT: a 170 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.7093 (m-30) REVERT: b 373 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8179 (mm) REVERT: c 87 MET cc_start: 0.6433 (ppp) cc_final: 0.5997 (pmm) outliers start: 56 outliers final: 38 residues processed: 240 average time/residue: 0.1795 time to fit residues: 56.5468 Evaluate side-chains 254 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 211 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 132 ASN Chi-restraints excluded: chain a residue 143 ASN Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 170 ASP Chi-restraints excluded: chain a residue 197 HIS Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 324 THR Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 341 GLU Chi-restraints excluded: chain b residue 342 VAL Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 373 LEU Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 52 ASN Chi-restraints excluded: chain c residue 99 THR Chi-restraints excluded: chain c residue 104 CYS Chi-restraints excluded: chain c residue 112 CYS Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 178 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 0.1980 chunk 77 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 310 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6856 Z= 0.168 Angle : 0.555 8.273 9230 Z= 0.287 Chirality : 0.042 0.139 1016 Planarity : 0.003 0.033 1192 Dihedral : 5.142 48.227 895 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 5.13 % Allowed : 27.11 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.28), residues: 812 helix: 0.83 (0.39), residues: 154 sheet: -0.39 (0.42), residues: 164 loop : -1.63 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 PHE 0.014 0.001 PHE C 13 TYR 0.026 0.001 TYR c 37 ARG 0.002 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 227 time to evaluate : 0.821 Fit side-chains REVERT: B 314 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6297 (ttp80) REVERT: B 373 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8044 (mm) REVERT: C 123 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7884 (m110) REVERT: a 170 ASP cc_start: 0.7343 (t0) cc_final: 0.7094 (m-30) REVERT: c 87 MET cc_start: 0.6663 (ppp) cc_final: 0.6285 (pmm) outliers start: 39 outliers final: 27 residues processed: 241 average time/residue: 0.1988 time to fit residues: 62.4341 Evaluate side-chains 246 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 216 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 341 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain c residue 99 THR Chi-restraints excluded: chain c residue 104 CYS Chi-restraints excluded: chain c residue 116 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 262 ASN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 52 ASN C 123 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6856 Z= 0.357 Angle : 0.621 7.513 9230 Z= 0.329 Chirality : 0.044 0.135 1016 Planarity : 0.003 0.037 1192 Dihedral : 5.391 46.733 895 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 6.97 % Allowed : 25.13 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.27), residues: 812 helix: 0.49 (0.39), residues: 154 sheet: -0.54 (0.42), residues: 164 loop : -1.73 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 335 HIS 0.004 0.001 HIS B 295 PHE 0.012 0.001 PHE C 13 TYR 0.019 0.002 TYR c 37 ARG 0.002 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 222 time to evaluate : 0.797 Fit side-chains REVERT: A 130 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: A 170 ASP cc_start: 0.7318 (t0) cc_final: 0.6985 (m-30) REVERT: B 373 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8087 (mm) REVERT: C 84 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8510 (mp) REVERT: a 170 ASP cc_start: 0.7348 (t0) cc_final: 0.7089 (m-30) REVERT: a 244 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8351 (mp) REVERT: b 373 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8187 (mm) REVERT: c 87 MET cc_start: 0.6676 (ppp) cc_final: 0.6286 (pmm) REVERT: c 106 LYS cc_start: 0.3472 (mttt) cc_final: 0.3191 (mmtt) outliers start: 53 outliers final: 40 residues processed: 239 average time/residue: 0.1883 time to fit residues: 58.9297 Evaluate side-chains 257 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 212 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 143 ASN Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 197 HIS Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 373 LEU Chi-restraints excluded: chain c residue 19 ILE Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 38 PHE Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 52 ASN Chi-restraints excluded: chain c residue 99 THR Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 178 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6856 Z= 0.223 Angle : 0.578 7.782 9230 Z= 0.307 Chirality : 0.042 0.132 1016 Planarity : 0.003 0.033 1192 Dihedral : 4.897 46.214 892 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.27 % Favored : 92.61 % Rotamer: Outliers : 5.92 % Allowed : 28.03 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.28), residues: 812 helix: 0.68 (0.39), residues: 154 sheet: -0.58 (0.42), residues: 164 loop : -1.64 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 335 HIS 0.003 0.001 HIS B 295 PHE 0.012 0.001 PHE C 13 TYR 0.034 0.001 TYR c 37 ARG 0.002 0.000 ARG a 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 225 time to evaluate : 0.841 Fit side-chains REVERT: A 170 ASP cc_start: 0.7274 (t0) cc_final: 0.7017 (m-30) REVERT: A 227 ASP cc_start: 0.8259 (t0) cc_final: 0.8049 (t0) REVERT: B 373 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8084 (mm) REVERT: C 192 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7815 (mm-30) REVERT: a 170 ASP cc_start: 0.7329 (t0) cc_final: 0.7091 (m-30) REVERT: c 87 MET cc_start: 0.6609 (ppp) cc_final: 0.6273 (pmm) outliers start: 45 outliers final: 34 residues processed: 242 average time/residue: 0.1783 time to fit residues: 57.0746 Evaluate side-chains 250 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 215 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 143 ASN Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 368 THR Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 38 PHE Chi-restraints excluded: chain c residue 99 THR Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 178 ASP Chi-restraints excluded: chain c residue 188 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6856 Z= 0.226 Angle : 0.591 8.465 9230 Z= 0.310 Chirality : 0.043 0.139 1016 Planarity : 0.003 0.033 1192 Dihedral : 4.905 44.596 892 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.77 % Favored : 93.10 % Rotamer: Outliers : 5.92 % Allowed : 28.42 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.28), residues: 812 helix: 0.77 (0.39), residues: 154 sheet: -0.67 (0.41), residues: 170 loop : -1.62 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 335 HIS 0.003 0.001 HIS B 295 PHE 0.012 0.001 PHE c 13 TYR 0.027 0.001 TYR c 37 ARG 0.001 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 214 time to evaluate : 0.817 Fit side-chains REVERT: A 170 ASP cc_start: 0.7307 (t0) cc_final: 0.7040 (m-30) REVERT: B 314 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6361 (ttp80) REVERT: B 373 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8086 (mm) REVERT: C 121 GLU cc_start: 0.6815 (pt0) cc_final: 0.6614 (pt0) REVERT: C 122 MET cc_start: 0.7304 (mmt) cc_final: 0.7067 (tpt) REVERT: C 192 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7803 (mm-30) REVERT: a 157 PHE cc_start: 0.8305 (m-80) cc_final: 0.7978 (m-80) REVERT: a 170 ASP cc_start: 0.7334 (t0) cc_final: 0.7080 (m-30) REVERT: c 87 MET cc_start: 0.6557 (ppp) cc_final: 0.6243 (pmm) outliers start: 45 outliers final: 38 residues processed: 234 average time/residue: 0.1821 time to fit residues: 56.3624 Evaluate side-chains 250 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 210 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 143 ASN Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 197 HIS Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 368 THR Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 38 PHE Chi-restraints excluded: chain c residue 99 THR Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 178 ASP Chi-restraints excluded: chain c residue 188 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6856 Z= 0.251 Angle : 0.601 8.495 9230 Z= 0.315 Chirality : 0.043 0.142 1016 Planarity : 0.003 0.033 1192 Dihedral : 4.902 43.974 892 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.14 % Favored : 92.73 % Rotamer: Outliers : 6.45 % Allowed : 28.42 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.28), residues: 812 helix: 0.79 (0.39), residues: 154 sheet: -0.69 (0.41), residues: 170 loop : -1.62 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 335 HIS 0.003 0.001 HIS B 295 PHE 0.010 0.001 PHE C 13 TYR 0.024 0.001 TYR c 37 ARG 0.003 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 203 time to evaluate : 0.843 Fit side-chains REVERT: A 130 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: A 170 ASP cc_start: 0.7311 (t0) cc_final: 0.7051 (m-30) REVERT: B 314 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6392 (ttp80) REVERT: B 373 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8096 (mm) REVERT: C 121 GLU cc_start: 0.6651 (pt0) cc_final: 0.6414 (pt0) REVERT: C 122 MET cc_start: 0.7332 (mmt) cc_final: 0.7122 (tpt) REVERT: C 192 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7891 (mm-30) REVERT: a 170 ASP cc_start: 0.7341 (t0) cc_final: 0.7091 (m-30) REVERT: c 87 MET cc_start: 0.6638 (ppp) cc_final: 0.6270 (pmm) outliers start: 49 outliers final: 37 residues processed: 226 average time/residue: 0.1889 time to fit residues: 56.7880 Evaluate side-chains 241 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 201 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 143 ASN Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 197 HIS Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 368 THR Chi-restraints excluded: chain c residue 19 ILE Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 123 ASN Chi-restraints excluded: chain c residue 178 ASP Chi-restraints excluded: chain c residue 188 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 0.0370 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6856 Z= 0.179 Angle : 0.593 8.893 9230 Z= 0.310 Chirality : 0.042 0.147 1016 Planarity : 0.003 0.031 1192 Dihedral : 4.704 43.566 892 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.77 % Favored : 93.10 % Rotamer: Outliers : 5.00 % Allowed : 30.00 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.28), residues: 812 helix: 0.97 (0.39), residues: 154 sheet: -0.58 (0.42), residues: 166 loop : -1.55 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 PHE 0.009 0.001 PHE C 13 TYR 0.025 0.001 TYR c 37 ARG 0.001 0.000 ARG a 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 210 time to evaluate : 0.814 Fit side-chains REVERT: A 130 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: A 170 ASP cc_start: 0.7300 (t0) cc_final: 0.7043 (m-30) REVERT: B 314 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6323 (ttp80) REVERT: B 373 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8041 (mm) REVERT: C 192 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7863 (mm-30) REVERT: a 157 PHE cc_start: 0.8259 (m-80) cc_final: 0.7976 (m-80) REVERT: a 170 ASP cc_start: 0.7308 (t0) cc_final: 0.7063 (m-30) outliers start: 38 outliers final: 31 residues processed: 225 average time/residue: 0.1902 time to fit residues: 56.1539 Evaluate side-chains 239 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 205 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 143 ASN Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 197 HIS Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 368 THR Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 178 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6856 Z= 0.211 Angle : 0.619 9.036 9230 Z= 0.322 Chirality : 0.043 0.144 1016 Planarity : 0.003 0.032 1192 Dihedral : 4.710 43.881 892 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.90 % Favored : 92.98 % Rotamer: Outliers : 4.61 % Allowed : 30.53 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.28), residues: 812 helix: 0.97 (0.39), residues: 154 sheet: -0.60 (0.42), residues: 166 loop : -1.56 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP b 335 HIS 0.003 0.001 HIS B 295 PHE 0.009 0.001 PHE C 13 TYR 0.027 0.001 TYR c 37 ARG 0.002 0.000 ARG a 269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 206 time to evaluate : 0.915 Fit side-chains REVERT: A 130 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: A 170 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.7046 (m-30) REVERT: B 373 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8020 (mm) REVERT: C 138 PHE cc_start: 0.7318 (m-80) cc_final: 0.7110 (m-80) REVERT: C 192 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7888 (mm-30) REVERT: a 157 PHE cc_start: 0.8271 (m-80) cc_final: 0.7993 (m-80) REVERT: a 170 ASP cc_start: 0.7311 (t0) cc_final: 0.7059 (m-30) outliers start: 35 outliers final: 30 residues processed: 221 average time/residue: 0.1876 time to fit residues: 54.5428 Evaluate side-chains 238 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 205 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 143 ASN Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 197 HIS Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 368 THR Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 178 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 65 optimal weight: 0.0670 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.197542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.127794 restraints weight = 7139.327| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.24 r_work: 0.3347 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6856 Z= 0.177 Angle : 0.604 9.232 9230 Z= 0.312 Chirality : 0.042 0.149 1016 Planarity : 0.003 0.030 1192 Dihedral : 4.573 43.702 892 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.65 % Favored : 93.23 % Rotamer: Outliers : 4.34 % Allowed : 31.45 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.28), residues: 812 helix: 1.07 (0.39), residues: 154 sheet: -0.57 (0.42), residues: 166 loop : -1.56 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 PHE 0.010 0.001 PHE C 13 TYR 0.025 0.001 TYR c 37 ARG 0.001 0.000 ARG a 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2136.40 seconds wall clock time: 39 minutes 10.62 seconds (2350.62 seconds total)