Starting phenix.real_space_refine on Fri Dec 8 02:53:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spb_40678/12_2023/8spb_40678.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spb_40678/12_2023/8spb_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_40678/12_2023/8spb_40678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spb_40678/12_2023/8spb_40678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spb_40678/12_2023/8spb_40678.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spb_40678/12_2023/8spb_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-1.21rc1-5172/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: 4.09, per 1000 atoms: 0.61 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: 2.44 Conformation dependent library (CDL) restraints added in 1.3 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: 0.82 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: 1.77 Time building geometry restraints manager: 2.65 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: 1.080 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: 0.000 Extract box with map and model: 4.420 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.390 Find NCS groups from input model: 0.330 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.250 ------------------------------------------------------------------------------- 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 : 0.865 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 244 average time/residue: 0.2028 time to fit residues: 64.0498 Evaluate side-chains 218 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 0.717 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0776 time to fit residues: 1.5274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 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: 2.9990 chunk 72 optimal weight: 6.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- 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: 0.7683 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6856 Z= 0.267 Angle : 0.574 7.174 9230 Z= 0.309 Chirality : 0.043 0.150 1016 Planarity : 0.004 0.043 1192 Dihedral : 4.428 22.995 890 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 5.39 % Allowed : 25.66 % Favored : 68.95 % 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: -1.19 (0.28), residues: 812 helix: 0.82 (0.39), residues: 152 sheet: -0.12 (0.42), residues: 160 loop : -1.62 (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 b 338 PHE 0.021 0.001 PHE C 13 TYR 0.019 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 257 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 216 time to evaluate : 0.760 Fit side-chains outliers start: 41 outliers final: 23 residues processed: 233 average time/residue: 0.1744 time to fit residues: 53.9113 Evaluate side-chains 228 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.0634 time to fit residues: 3.6767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 0.0050 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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: 0.7655 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6856 Z= 0.206 Angle : 0.561 8.511 9230 Z= 0.294 Chirality : 0.043 0.141 1016 Planarity : 0.003 0.035 1192 Dihedral : 4.290 21.814 890 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.50 % Allowed : 27.24 % Favored : 70.26 % 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: -1.18 (0.28), residues: 812 helix: 0.95 (0.40), residues: 152 sheet: -0.25 (0.42), residues: 164 loop : -1.61 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP b 335 HIS 0.004 0.001 HIS b 338 PHE 0.016 0.001 PHE C 13 TYR 0.011 0.001 TYR c 37 ARG 0.002 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 234 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 215 time to evaluate : 0.751 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 223 average time/residue: 0.1863 time to fit residues: 54.5824 Evaluate side-chains 224 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 212 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0689 time to fit residues: 2.5944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 30.0000 chunk 77 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 b 310 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6856 Z= 0.362 Angle : 0.611 7.300 9230 Z= 0.327 Chirality : 0.044 0.136 1016 Planarity : 0.004 0.045 1192 Dihedral : 4.696 22.701 890 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 5.66 % Allowed : 26.18 % Favored : 68.16 % 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: -1.45 (0.27), residues: 812 helix: 0.56 (0.39), residues: 154 sheet: -0.51 (0.41), 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 0.006 0.001 HIS a 197 PHE 0.013 0.001 PHE C 13 TYR 0.030 0.002 TYR c 37 ARG 0.010 0.000 ARG B 314 *********************** 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 264 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 221 time to evaluate : 0.720 Fit side-chains outliers start: 43 outliers final: 25 residues processed: 234 average time/residue: 0.1927 time to fit residues: 58.8589 Evaluate side-chains 235 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 210 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0842 time to fit residues: 4.5369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 31 optimal weight: 0.0000 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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: 0.7651 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6856 Z= 0.183 Angle : 0.575 8.217 9230 Z= 0.298 Chirality : 0.042 0.132 1016 Planarity : 0.003 0.031 1192 Dihedral : 4.339 21.262 890 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.97 % Allowed : 27.24 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.28), residues: 812 helix: 0.87 (0.39), residues: 154 sheet: -0.55 (0.41), residues: 164 loop : -1.61 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP b 335 HIS 0.004 0.001 HIS b 338 PHE 0.012 0.001 PHE C 13 TYR 0.017 0.001 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 235 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 220 time to evaluate : 0.850 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 225 average time/residue: 0.1801 time to fit residues: 53.8998 Evaluate side-chains 216 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 207 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1028 time to fit residues: 2.5965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN C 52 ASN a 256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6856 Z= 0.178 Angle : 0.576 7.927 9230 Z= 0.298 Chirality : 0.042 0.143 1016 Planarity : 0.003 0.031 1192 Dihedral : 4.307 21.506 890 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.65 % Favored : 93.23 % Rotamer: Outliers : 2.63 % Allowed : 29.47 % 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: -1.28 (0.28), residues: 812 helix: 0.99 (0.39), residues: 154 sheet: -0.65 (0.41), residues: 166 loop : -1.60 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 335 HIS 0.003 0.001 HIS b 338 PHE 0.011 0.001 PHE c 13 TYR 0.034 0.001 TYR c 37 ARG 0.002 0.000 ARG A 269 *********************** 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 230 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 210 time to evaluate : 0.604 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 217 average time/residue: 0.1627 time to fit residues: 47.0045 Evaluate side-chains 222 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 208 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0856 time to fit residues: 3.5170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7641 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6856 Z= 0.193 Angle : 0.584 8.606 9230 Z= 0.303 Chirality : 0.042 0.142 1016 Planarity : 0.003 0.032 1192 Dihedral : 4.282 21.140 890 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.53 % Favored : 93.35 % Rotamer: Outliers : 1.18 % Allowed : 30.39 % Favored : 68.42 % 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: -1.26 (0.28), residues: 812 helix: 1.07 (0.39), residues: 154 sheet: -0.67 (0.41), residues: 166 loop : -1.60 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 335 HIS 0.003 0.001 HIS b 338 PHE 0.011 0.001 PHE C 13 TYR 0.027 0.001 TYR c 37 ARG 0.002 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 223 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 214 time to evaluate : 0.861 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 216 average time/residue: 0.2156 time to fit residues: 61.7441 Evaluate side-chains 210 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 205 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0829 time to fit residues: 1.9425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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: 0.7738 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6856 Z= 0.356 Angle : 0.656 7.848 9230 Z= 0.343 Chirality : 0.045 0.157 1016 Planarity : 0.004 0.037 1192 Dihedral : 4.721 21.735 890 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.02 % Favored : 92.86 % Rotamer: Outliers : 2.50 % Allowed : 30.00 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.27), residues: 812 helix: 0.54 (0.38), residues: 154 sheet: -0.76 (0.41), residues: 170 loop : -1.74 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP b 335 HIS 0.006 0.001 HIS a 197 PHE 0.011 0.001 PHE b 300 TYR 0.028 0.002 TYR c 37 ARG 0.003 0.000 ARG c 49 *********************** 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 225 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 206 time to evaluate : 0.856 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 210 average time/residue: 0.1771 time to fit residues: 49.7757 Evaluate side-chains 219 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0667 time to fit residues: 2.6613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6856 Z= 0.285 Angle : 0.650 8.480 9230 Z= 0.341 Chirality : 0.044 0.136 1016 Planarity : 0.003 0.035 1192 Dihedral : 4.595 21.876 890 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.90 % Favored : 92.98 % Rotamer: Outliers : 0.92 % Allowed : 30.92 % Favored : 68.16 % 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: -1.57 (0.27), residues: 812 helix: 0.60 (0.38), residues: 154 sheet: -0.80 (0.41), residues: 170 loop : -1.74 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP b 335 HIS 0.004 0.001 HIS a 197 PHE 0.011 0.001 PHE C 13 TYR 0.028 0.001 TYR c 37 ARG 0.002 0.000 ARG A 259 *********************** 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 216 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 209 time to evaluate : 0.808 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 211 average time/residue: 0.1826 time to fit residues: 51.2812 Evaluate side-chains 210 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 205 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0676 time to fit residues: 1.7906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.7651 moved from start: 0.2951 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= 0.198 Angle : 0.634 8.796 9230 Z= 0.329 Chirality : 0.043 0.144 1016 Planarity : 0.003 0.033 1192 Dihedral : 4.359 21.648 890 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.02 % Favored : 92.86 % Rotamer: Outliers : 0.66 % Allowed : 32.76 % Favored : 66.58 % 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: -1.42 (0.28), residues: 812 helix: 0.88 (0.38), residues: 154 sheet: -0.76 (0.41), residues: 166 loop : -1.68 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 335 HIS 0.003 0.001 HIS b 338 PHE 0.009 0.001 PHE c 13 TYR 0.027 0.001 TYR c 37 ARG 0.001 0.000 ARG a 131 ********************** 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 200 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 195 time to evaluate : 0.813 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 195 average time/residue: 0.1826 time to fit residues: 47.7106 Evaluate side-chains 194 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 191 time to evaluate : 0.769 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0756 time to fit residues: 1.5134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.194209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.123800 restraints weight = 7175.171| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.29 r_work: 0.3297 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6856 Z= 0.226 Angle : 0.637 8.548 9230 Z= 0.333 Chirality : 0.043 0.139 1016 Planarity : 0.003 0.033 1192 Dihedral : 4.355 22.077 890 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.77 % Favored : 93.10 % Rotamer: Outliers : 0.39 % Allowed : 32.76 % Favored : 66.84 % 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: -1.36 (0.28), residues: 812 helix: 0.95 (0.39), residues: 154 sheet: -0.73 (0.42), residues: 166 loop : -1.65 (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 b 338 PHE 0.012 0.001 PHE c 13 TYR 0.028 0.001 TYR c 37 ARG 0.003 0.000 ARG a 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2069.20 seconds wall clock time: 41 minutes 51.28 seconds (2511.28 seconds total)