Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 23:09:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/10_2023/8cvn_27010_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/10_2023/8cvn_27010.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/10_2023/8cvn_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_27010/10_2023/8cvn_27010_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/10_2023/8cvn_27010_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/10_2023/8cvn_27010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/10_2023/8cvn_27010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/10_2023/8cvn_27010_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvn_27010/10_2023/8cvn_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-1.21rc1-5097/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: 2.88, per 1000 atoms: 0.71 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: 1.61 Conformation dependent library (CDL) restraints added in 630.2 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: 0.98 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: 1.13 Time building geometry restraints manager: 1.70 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: 2023 16.30 - 32.61: 260 32.61 - 48.91: 82 48.91 - 65.21: 31 65.21 - 81.51: 12 Dihedral angle restraints: 2408 sinusoidal: 954 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 2405 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 26.980 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.130 Find NCS groups from input model: 0.190 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.870 ------------------------------------------------------------------------------- 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 : 17.971 81.509 1480 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 *********************** 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 : 0.532 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 77 average time/residue: 1.6202 time to fit residues: 128.0532 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6327 ------------------------------------------------------------------------------- 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: 0.8354 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4128 Z= 0.187 Angle : 0.836 24.062 5604 Z= 0.336 Chirality : 0.042 0.126 634 Planarity : 0.003 0.045 710 Dihedral : 5.455 52.251 566 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.47 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: 1.52 (0.39), residues: 508 helix: 1.79 (0.35), residues: 260 sheet: 0.67 (0.49), residues: 108 loop : -0.10 (0.52), residues: 140 *********************** 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 54 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 0.467 Fit side-chains outliers start: 14 outliers final: 3 residues processed: 47 average time/residue: 1.5448 time to fit residues: 74.9564 Evaluate side-chains 39 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.477 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.0421 time to fit residues: 0.7609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 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: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8431 moved from start: 0.2811 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= 0.229 Angle : 0.831 23.805 5604 Z= 0.334 Chirality : 0.041 0.129 634 Planarity : 0.004 0.044 710 Dihedral : 5.181 46.366 566 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.42 % Allowed : 21.50 % 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: 1.51 (0.39), residues: 508 helix: 1.86 (0.35), residues: 258 sheet: 0.59 (0.49), residues: 108 loop : -0.16 (0.52), residues: 142 *********************** 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 53 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.486 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 49 average time/residue: 1.2459 time to fit residues: 63.4454 Evaluate side-chains 46 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.459 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.0573 time to fit residues: 0.8874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 5 optimal weight: 0.0870 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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: 0.8432 moved from start: 0.3041 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= 0.197 Angle : 0.812 23.765 5604 Z= 0.322 Chirality : 0.040 0.126 634 Planarity : 0.004 0.043 710 Dihedral : 5.179 44.887 566 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.38 % Allowed : 21.26 % Favored : 75.36 % 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: 1.58 (0.39), residues: 508 helix: 1.94 (0.35), residues: 258 sheet: 0.60 (0.49), residues: 108 loop : -0.15 (0.52), residues: 142 *********************** 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 57 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 43 time to evaluate : 0.467 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 50 average time/residue: 1.1365 time to fit residues: 59.2599 Evaluate side-chains 54 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.514 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.2474 time to fit residues: 2.0071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 41 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.0570 chunk 28 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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: 0.8429 moved from start: 0.3137 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 : 0.803 23.763 5604 Z= 0.315 Chirality : 0.040 0.127 634 Planarity : 0.004 0.043 710 Dihedral : 5.239 45.228 566 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.62 % Allowed : 21.01 % Favored : 75.36 % 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: 1.58 (0.39), residues: 508 helix: 1.97 (0.35), residues: 258 sheet: 0.58 (0.48), residues: 108 loop : -0.20 (0.51), residues: 142 *********************** 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 61 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 46 time to evaluate : 0.457 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 53 average time/residue: 1.0250 time to fit residues: 56.9343 Evaluate side-chains 52 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.500 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 0.3015 time to fit residues: 2.2693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8447 moved from start: 0.3180 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= 0.205 Angle : 0.808 23.809 5604 Z= 0.318 Chirality : 0.040 0.126 634 Planarity : 0.004 0.044 710 Dihedral : 5.415 49.965 566 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.14 % Allowed : 22.46 % Favored : 74.40 % 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: 1.93 (0.35), residues: 258 sheet: 0.56 (0.49), residues: 108 loop : -0.20 (0.51), residues: 142 *********************** 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 55 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.462 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 48 average time/residue: 1.1824 time to fit residues: 59.1458 Evaluate side-chains 50 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.526 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.0673 time to fit residues: 1.0511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 overall best weight: 0.6560 ------------------------------------------------------------------------------- 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: 0.8454 moved from start: 0.3211 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 : 0.810 23.709 5604 Z= 0.319 Chirality : 0.040 0.127 634 Planarity : 0.004 0.045 710 Dihedral : 5.615 55.649 566 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.90 % Allowed : 22.46 % 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: 1.52 (0.39), residues: 508 helix: 1.91 (0.35), residues: 258 sheet: 0.55 (0.49), residues: 108 loop : -0.20 (0.51), residues: 142 *********************** 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 53 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.428 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 47 average time/residue: 1.1689 time to fit residues: 57.2908 Evaluate side-chains 51 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.444 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.2598 time to fit residues: 2.0420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.0040 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 0.0370 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 overall best weight: 0.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4128 Z= 0.154 Angle : 0.795 23.776 5604 Z= 0.308 Chirality : 0.039 0.124 634 Planarity : 0.004 0.046 710 Dihedral : 5.653 58.414 566 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.93 % Allowed : 22.95 % 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: 1.62 (0.39), residues: 508 helix: 2.03 (0.35), residues: 258 sheet: 0.54 (0.48), residues: 108 loop : -0.20 (0.51), residues: 142 *********************** 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 49 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.467 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 47 average time/residue: 1.1309 time to fit residues: 55.5089 Evaluate side-chains 48 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.499 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.0821 time to fit residues: 0.8276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.0670 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.0040 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 0.0270 chunk 39 optimal weight: 0.1980 overall best weight: 0.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4128 Z= 0.116 Angle : 0.780 23.735 5604 Z= 0.298 Chirality : 0.039 0.120 634 Planarity : 0.004 0.047 710 Dihedral : 5.228 52.425 566 Min Nonbonded Distance : 2.279 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: 1.83 (0.39), residues: 508 helix: 2.23 (0.36), residues: 256 sheet: 0.54 (0.48), residues: 112 loop : -0.06 (0.51), residues: 140 *********************** 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 50 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.466 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 48 average time/residue: 1.0497 time to fit residues: 52.8100 Evaluate side-chains 47 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.6452 time to fit residues: 2.0094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8451 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4128 Z= 0.224 Angle : 0.810 23.654 5604 Z= 0.319 Chirality : 0.040 0.126 634 Planarity : 0.004 0.045 710 Dihedral : 5.082 43.180 566 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.69 % Allowed : 22.46 % 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: 1.54 (0.39), residues: 508 helix: 1.99 (0.35), residues: 258 sheet: 0.58 (0.48), residues: 108 loop : -0.37 (0.50), residues: 142 ********************** 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 48 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.492 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 46 average time/residue: 1.0284 time to fit residues: 49.6324 Evaluate side-chains 48 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.507 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.0884 time to fit residues: 0.8340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1980 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 overall best weight: 0.3898 ------------------------------------------------------------------------------- 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 = 0.3128 r_free = 0.3128 target = 0.090146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.082805 restraints weight = 6002.317| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.01 r_work: 0.2870 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4128 Z= 0.151 Angle : 0.789 23.737 5604 Z= 0.305 Chirality : 0.039 0.122 634 Planarity : 0.004 0.046 710 Dihedral : 4.720 43.996 566 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.93 % Allowed : 22.71 % Favored : 75.36 % 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: 1.58 (0.39), residues: 508 helix: 2.08 (0.35), residues: 258 sheet: 0.57 (0.48), residues: 108 loop : -0.44 (0.49), residues: 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2155.80 seconds wall clock time: 39 minutes 9.92 seconds (2349.92 seconds total)