Starting phenix.real_space_refine on Sun Mar 10 18:46:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/03_2024/8cvn_27010_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/03_2024/8cvn_27010.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/03_2024/8cvn_27010_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/03_2024/8cvn_27010_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/03_2024/8cvn_27010_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/03_2024/8cvn_27010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/03_2024/8cvn_27010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/03_2024/8cvn_27010_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/03_2024/8cvn_27010_updated.pdb" } resolution = 2.4 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 30 5.16 5 C 2560 2.51 5 N 690 2.21 5 O 770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 36": "OD1" <-> "OD2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A ASP 73": "OD1" <-> "OD2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4054 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 256, 1955 Classifications: {'peptide': 256} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 249} Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 256, 1955 Classifications: {'peptide': 256} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 249} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'NAI': 1, 'SWL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'NAI': 1, 'SWL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.04, per 1000 atoms: 0.75 Number of scatterers: 4054 At special positions: 0 Unit cell: (95.16, 69.16, 56.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 4 15.00 O 770 8.00 N 690 7.00 C 2560 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: 1.79 Conformation dependent library (CDL) restraints added in 762.6 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 928 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 2 sheets defined 53.1% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 17 through 28 Processing helix chain 'A' and resid 39 through 51 Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 68 through 82 Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 109 through 122 removed outlier: 3.650A pdb=" N TYR A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 149 through 172 removed outlier: 3.654A pdb=" N LEU A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 197 through 217 removed outlier: 8.215A pdb=" N GLN A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N TYR A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE A 204 " --> pdb=" O MET A 200 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N TYR A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 234 removed outlier: 3.755A pdb=" N ALA A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 227 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 28 Processing helix chain 'B' and resid 39 through 51 Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 68 through 82 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 109 through 122 removed outlier: 3.552A pdb=" N TYR B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 149 through 172 removed outlier: 3.654A pdb=" N LEU B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 195 Processing helix chain 'B' and resid 197 through 217 removed outlier: 8.235A pdb=" N GLN B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N TYR B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE B 204 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLU B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N TYR B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS B 207 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE B 210 " --> pdb=" O TYR B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 234 removed outlier: 3.545A pdb=" N GLY B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 251 through 253 removed outlier: 9.086A pdb=" N MET A 243 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA A 180 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ILE A 245 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N CYS A 182 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY A 131 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASN A 179 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 133 " --> pdb=" O ASN A 179 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ILE A 181 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN A 135 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER A 137 " --> pdb=" O PRO A 183 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS A 31 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL A 10 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA A 33 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 251 through 253 removed outlier: 9.087A pdb=" N MET B 243 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA B 180 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ILE B 245 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N CYS B 182 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY B 131 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ASN B 179 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE B 133 " --> pdb=" O ASN B 179 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ILE B 181 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN B 135 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER B 137 " --> pdb=" O PRO B 183 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS B 31 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL B 10 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA B 33 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 36 " --> pdb=" O ILE B 61 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 522 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: 1.15 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 686 1.30 - 1.43: 998 1.43 - 1.55: 2380 1.55 - 1.68: 16 1.68 - 1.81: 48 Bond restraints: 4128 Sorted by residual: bond pdb=" C2 SWL A 302 " pdb=" N1 SWL A 302 " ideal model delta sigma weight residual 1.567 1.360 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C2 SWL B 302 " pdb=" N1 SWL B 302 " ideal model delta sigma weight residual 1.567 1.361 0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C1 SWL B 302 " pdb=" S1 SWL B 302 " ideal model delta sigma weight residual 1.519 1.690 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C1 SWL A 302 " pdb=" S1 SWL A 302 " ideal model delta sigma weight residual 1.519 1.689 -0.170 2.00e-02 2.50e+03 7.19e+01 bond pdb=" C7 SWL B 302 " pdb=" C9 SWL B 302 " ideal model delta sigma weight residual 1.617 1.464 0.153 2.00e-02 2.50e+03 5.84e+01 ... (remaining 4123 not shown) Histogram of bond angle deviations from ideal: 97.41 - 104.86: 79 104.86 - 112.30: 1985 112.30 - 119.74: 1618 119.74 - 127.18: 1868 127.18 - 134.62: 54 Bond angle restraints: 5604 Sorted by residual: angle pdb=" N SER A 123 " pdb=" CA ASER A 123 " pdb=" C SER A 123 " ideal model delta sigma weight residual 110.23 123.25 -13.02 1.45e+00 4.76e-01 8.06e+01 angle pdb=" N SER B 123 " pdb=" CA ASER B 123 " pdb=" C SER B 123 " ideal model delta sigma weight residual 110.23 123.05 -12.82 1.45e+00 4.76e-01 7.81e+01 angle pdb=" C10 SWL B 302 " pdb=" C9 SWL B 302 " pdb=" N5 SWL B 302 " ideal model delta sigma weight residual 95.45 120.44 -24.99 3.00e+00 1.11e-01 6.94e+01 angle pdb=" C10 SWL A 302 " pdb=" C9 SWL A 302 " pdb=" N5 SWL A 302 " ideal model delta sigma weight residual 95.45 120.40 -24.95 3.00e+00 1.11e-01 6.92e+01 angle pdb=" C7 SWL A 302 " pdb=" C9 SWL A 302 " pdb=" N5 SWL A 302 " ideal model delta sigma weight residual 100.36 123.86 -23.50 3.00e+00 1.11e-01 6.13e+01 ... (remaining 5599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 2087 16.30 - 32.61: 284 32.61 - 48.91: 90 48.91 - 65.21: 37 65.21 - 81.51: 14 Dihedral angle restraints: 2512 sinusoidal: 1058 harmonic: 1454 Sorted by residual: dihedral pdb=" C PRO A 222 " pdb=" N PRO A 222 " pdb=" CA PRO A 222 " pdb=" CB PRO A 222 " ideal model delta harmonic sigma weight residual -120.70 -133.98 13.28 0 2.50e+00 1.60e-01 2.82e+01 dihedral pdb=" C ASN B 173 " pdb=" N ASN B 173 " pdb=" CA ASN B 173 " pdb=" CB ASN B 173 " ideal model delta harmonic sigma weight residual -122.60 -134.78 12.18 0 2.50e+00 1.60e-01 2.37e+01 dihedral pdb=" C ASN A 173 " pdb=" N ASN A 173 " pdb=" CA ASN A 173 " pdb=" CB ASN A 173 " ideal model delta harmonic sigma weight residual -122.60 -134.33 11.73 0 2.50e+00 1.60e-01 2.20e+01 ... (remaining 2509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 583 0.124 - 0.248: 44 0.248 - 0.372: 3 0.372 - 0.496: 3 0.496 - 0.620: 1 Chirality restraints: 634 Sorted by residual: chirality pdb=" CA PRO A 222 " pdb=" N PRO A 222 " pdb=" C PRO A 222 " pdb=" CB PRO A 222 " both_signs ideal model delta sigma weight residual False 2.72 2.10 0.62 2.00e-01 2.50e+01 9.62e+00 chirality pdb=" CA ASER A 123 " pdb=" N SER A 123 " pdb=" C SER A 123 " pdb=" CB ASER A 123 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA ASER B 123 " pdb=" N SER B 123 " pdb=" C SER B 123 " pdb=" CB ASER B 123 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.86e+00 ... (remaining 631 not shown) Planarity restraints: 710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 195 " -0.016 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C GLU B 195 " 0.058 2.00e-02 2.50e+03 pdb=" O GLU B 195 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS B 196 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 195 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C GLU A 195 " -0.049 2.00e-02 2.50e+03 pdb=" O GLU A 195 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 196 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 152 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C CYS B 152 " -0.044 2.00e-02 2.50e+03 pdb=" O CYS B 152 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA B 153 " 0.015 2.00e-02 2.50e+03 ... (remaining 707 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 2062 3.00 - 3.47: 3991 3.47 - 3.95: 6708 3.95 - 4.42: 8029 4.42 - 4.90: 12362 Nonbonded interactions: 33152 Sorted by model distance: nonbonded pdb=" N CYS B 182 " pdb=" O MET B 243 " model vdw 2.524 2.520 nonbonded pdb=" N CYS A 182 " pdb=" O MET A 243 " model vdw 2.524 2.520 nonbonded pdb=" O LEU B 178 " pdb=" OD1 ASN B 179 " model vdw 2.536 3.040 nonbonded pdb=" O LEU A 178 " pdb=" OD1 ASN A 179 " model vdw 2.536 3.040 nonbonded pdb=" O GLN B 70 " pdb=" OG1 THR B 74 " model vdw 2.547 2.440 ... (remaining 33147 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 'B' } 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=0.50 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: 5.910 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: 27.160 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 16.980 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.014 0.207 4128 Z= 0.846 Angle : 1.534 24.989 5604 Z= 0.922 Chirality : 0.077 0.620 634 Planarity : 0.005 0.034 710 Dihedral : 18.397 81.509 1584 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.21 % Allowed : 19.81 % Favored : 78.99 % Cbeta Deviations : 0.65 % 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: 0.60 (0.37), residues: 508 helix: 1.02 (0.33), residues: 258 sheet: 0.63 (0.47), residues: 108 loop : -0.78 (0.47), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 100 HIS 0.004 0.001 HIS A 156 PHE 0.035 0.003 PHE A 75 TYR 0.019 0.002 TYR A 121 ARG 0.002 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.480 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 77 average time/residue: 1.6265 time to fit residues: 128.4721 Evaluate side-chains 38 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 90 ASN A 148 GLN B 81 HIS B 90 ASN B 148 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4128 Z= 0.188 Angle : 0.835 24.050 5604 Z= 0.336 Chirality : 0.042 0.123 634 Planarity : 0.003 0.045 710 Dihedral : 9.258 75.947 670 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.38 % Allowed : 20.77 % Favored : 75.85 % 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: 1.53 (0.39), residues: 508 helix: 1.82 (0.35), residues: 260 sheet: 0.68 (0.49), residues: 108 loop : -0.13 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 100 HIS 0.003 0.001 HIS A 252 PHE 0.007 0.001 PHE B 82 TYR 0.008 0.001 TYR B 151 ARG 0.005 0.001 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 41 time to evaluate : 0.426 Fit side-chains outliers start: 14 outliers final: 3 residues processed: 48 average time/residue: 1.4817 time to fit residues: 73.4534 Evaluate side-chains 41 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 58 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4128 Z= 0.263 Angle : 0.844 23.912 5604 Z= 0.342 Chirality : 0.041 0.130 634 Planarity : 0.004 0.043 710 Dihedral : 9.191 79.220 670 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.90 % Allowed : 21.26 % Favored : 75.85 % 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: 1.46 (0.39), residues: 508 helix: 1.79 (0.34), residues: 258 sheet: 0.62 (0.49), residues: 108 loop : -0.17 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 100 HIS 0.003 0.001 HIS A 1 PHE 0.006 0.001 PHE A 60 TYR 0.008 0.001 TYR B 151 ARG 0.003 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.513 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 51 average time/residue: 1.2748 time to fit residues: 67.4715 Evaluate side-chains 49 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 58 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 48 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4128 Z= 0.214 Angle : 0.819 23.763 5604 Z= 0.326 Chirality : 0.040 0.126 634 Planarity : 0.004 0.043 710 Dihedral : 9.132 83.561 670 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.66 % Allowed : 21.26 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.39), residues: 508 helix: 1.89 (0.35), residues: 258 sheet: 0.62 (0.49), residues: 108 loop : -0.16 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 100 HIS 0.002 0.001 HIS A 252 PHE 0.005 0.001 PHE A 60 TYR 0.007 0.001 TYR B 216 ARG 0.005 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.500 Fit side-chains REVERT: B 84 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7429 (ptt90) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 1.1437 time to fit residues: 56.0956 Evaluate side-chains 52 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 248 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 9 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4128 Z= 0.195 Angle : 0.809 23.760 5604 Z= 0.318 Chirality : 0.040 0.126 634 Planarity : 0.004 0.043 710 Dihedral : 9.240 88.765 670 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.62 % Allowed : 21.50 % Favored : 74.88 % 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: 1.55 (0.39), residues: 508 helix: 1.91 (0.35), residues: 258 sheet: 0.57 (0.49), residues: 108 loop : -0.16 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 100 HIS 0.002 0.001 HIS B 252 PHE 0.005 0.001 PHE A 82 TYR 0.006 0.001 TYR B 151 ARG 0.004 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 47 time to evaluate : 0.482 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 53 average time/residue: 1.0527 time to fit residues: 58.0904 Evaluate side-chains 52 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 248 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 0.0670 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4128 Z= 0.179 Angle : 0.804 23.837 5604 Z= 0.314 Chirality : 0.040 0.125 634 Planarity : 0.004 0.045 710 Dihedral : 9.096 83.087 670 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.42 % Allowed : 22.46 % Favored : 75.12 % 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 (0.39), residues: 508 helix: 1.95 (0.35), residues: 258 sheet: 0.58 (0.49), residues: 108 loop : -0.20 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 100 HIS 0.003 0.001 HIS A 252 PHE 0.004 0.001 PHE A 82 TYR 0.006 0.001 TYR B 151 ARG 0.004 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.474 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 47 average time/residue: 1.0321 time to fit residues: 50.8384 Evaluate side-chains 52 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 248 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4128 Z= 0.195 Angle : 0.807 23.683 5604 Z= 0.316 Chirality : 0.040 0.126 634 Planarity : 0.004 0.045 710 Dihedral : 8.915 76.141 670 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.38 % Allowed : 22.46 % Favored : 74.15 % 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: 1.56 (0.39), residues: 508 helix: 1.95 (0.35), residues: 258 sheet: 0.54 (0.49), residues: 108 loop : -0.21 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 100 HIS 0.002 0.001 HIS A 252 PHE 0.005 0.001 PHE A 60 TYR 0.006 0.001 TYR B 151 ARG 0.004 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.472 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 50 average time/residue: 1.0214 time to fit residues: 53.4456 Evaluate side-chains 53 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 248 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.0270 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.0870 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS B 252 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4128 Z= 0.133 Angle : 0.792 23.725 5604 Z= 0.305 Chirality : 0.039 0.122 634 Planarity : 0.004 0.046 710 Dihedral : 8.598 67.808 670 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.17 % Allowed : 22.95 % Favored : 74.88 % 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: 1.69 (0.39), residues: 508 helix: 2.11 (0.36), residues: 258 sheet: 0.56 (0.48), residues: 108 loop : -0.22 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 100 HIS 0.003 0.001 HIS A 252 PHE 0.004 0.001 PHE A 82 TYR 0.006 0.001 TYR B 151 ARG 0.004 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.524 Fit side-chains REVERT: A 211 LYS cc_start: 0.7776 (mtpp) cc_final: 0.7425 (ttmt) outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 0.9700 time to fit residues: 49.8126 Evaluate side-chains 50 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 248 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 39 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4128 Z= 0.201 Angle : 0.807 23.674 5604 Z= 0.316 Chirality : 0.040 0.126 634 Planarity : 0.004 0.045 710 Dihedral : 8.701 68.694 670 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.17 % Allowed : 22.95 % Favored : 74.88 % 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 (0.39), residues: 508 helix: 2.03 (0.35), residues: 258 sheet: 0.50 (0.48), residues: 108 loop : -0.29 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 100 HIS 0.002 0.001 HIS A 156 PHE 0.004 0.001 PHE A 60 TYR 0.006 0.001 TYR A 151 ARG 0.003 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.495 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 48 average time/residue: 1.0148 time to fit residues: 51.1303 Evaluate side-chains 52 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 248 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.0070 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.0980 chunk 39 optimal weight: 0.0070 chunk 16 optimal weight: 0.5980 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4128 Z= 0.125 Angle : 0.786 23.763 5604 Z= 0.302 Chirality : 0.039 0.121 634 Planarity : 0.004 0.046 710 Dihedral : 8.257 62.622 670 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.42 % Allowed : 22.95 % Favored : 74.64 % 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: 1.70 (0.39), residues: 508 helix: 2.20 (0.36), residues: 256 sheet: 0.55 (0.48), residues: 108 loop : -0.32 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 100 HIS 0.002 0.000 HIS A 252 PHE 0.002 0.001 PHE B 60 TYR 0.005 0.000 TYR A 151 ARG 0.003 0.000 ARG B 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.484 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 50 average time/residue: 1.0661 time to fit residues: 55.8046 Evaluate side-chains 53 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 248 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.0070 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.0070 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.090715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.083293 restraints weight = 5961.884| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.00 r_work: 0.2884 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4128 Z= 0.144 Angle : 0.790 23.732 5604 Z= 0.305 Chirality : 0.039 0.123 634 Planarity : 0.004 0.046 710 Dihedral : 8.227 62.496 670 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.69 % Allowed : 23.19 % Favored : 75.12 % 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: 1.69 (0.39), residues: 508 helix: 2.19 (0.36), residues: 256 sheet: 0.42 (0.48), residues: 112 loop : -0.23 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 100 HIS 0.002 0.001 HIS A 252 PHE 0.004 0.001 PHE B 82 TYR 0.006 0.001 TYR A 151 ARG 0.003 0.000 ARG B 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2192.85 seconds wall clock time: 40 minutes 33.20 seconds (2433.20 seconds total)