Starting phenix.real_space_refine on Thu Dec 7 21:38:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez7_28729/12_2023/8ez7_28729.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez7_28729/12_2023/8ez7_28729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez7_28729/12_2023/8ez7_28729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez7_28729/12_2023/8ez7_28729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez7_28729/12_2023/8ez7_28729.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez7_28729/12_2023/8ez7_28729.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.202 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3065 2.51 5 N 845 2.21 5 O 989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 33": "OE1" <-> "OE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A ASP 309": "OD1" <-> "OD2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ASP 460": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4927 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 833 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 9, 'TRANS': 100} Chain: "A" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2996 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 372} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.46, per 1000 atoms: 0.70 Number of scatterers: 4927 At special positions: 0 Unit cell: (95.4, 83.74, 89.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 989 8.00 N 845 7.00 C 3065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.02 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 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 Links applied ALPHA1-2 " MAN B 4 " - " MAN B 5 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 502 " - " ASN A 146 " " NAG A 503 " - " ASN A 329 " " NAG A 504 " - " ASN A 234 " " NAG B 1 " - " ASN A 200 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 919.8 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1120 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 12 sheets defined 4.8% alpha, 45.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.744A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.585A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.547A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.784A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.788A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.412A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.976A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.627A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N LEU L 28 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N SER L 65 " --> pdb=" O LEU L 28 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.090A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.648A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 124 removed outlier: 5.343A pdb=" N THR A 138 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N ARG A 118 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLN A 136 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU A 134 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL A 122 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE A 132 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N CYS A 124 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A 130 " --> pdb=" O CYS A 124 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.276A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.733A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.637A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.321A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.561A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER A 372 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS A 378 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) 169 hydrogen bonds defined for protein. 429 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: 1.57 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1609 1.34 - 1.46: 1256 1.46 - 1.58: 2139 1.58 - 1.70: 0 1.70 - 1.81: 34 Bond restraints: 5038 Sorted by residual: bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C5 MAN B 5 " pdb=" O5 MAN B 5 " ideal model delta sigma weight residual 1.418 1.450 -0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C1 MAN B 5 " pdb=" O5 MAN B 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.55e+00 bond pdb=" C1 MAN B 5 " pdb=" C2 MAN B 5 " ideal model delta sigma weight residual 1.526 1.556 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta sigma weight residual 1.469 1.487 -0.018 1.28e-02 6.10e+03 2.03e+00 ... (remaining 5033 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.15: 110 106.15 - 113.11: 2738 113.11 - 120.07: 1641 120.07 - 127.03: 2278 127.03 - 133.99: 69 Bond angle restraints: 6836 Sorted by residual: angle pdb=" C PRO L 95 " pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta sigma weight residual 119.84 115.33 4.51 1.25e+00 6.40e-01 1.30e+01 angle pdb=" C ARG A 430 " pdb=" N LYS A 431 " pdb=" CA LYS A 431 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 angle pdb=" N PRO L 95 " pdb=" CA PRO L 95 " pdb=" C PRO L 95 " ideal model delta sigma weight residual 110.70 113.47 -2.77 1.22e+00 6.72e-01 5.14e+00 angle pdb=" C3 BMA B 3 " pdb=" C2 BMA B 3 " pdb=" O2 BMA B 3 " ideal model delta sigma weight residual 112.95 106.51 6.44 3.00e+00 1.11e-01 4.61e+00 angle pdb=" N CYS A 337 " pdb=" CA CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sigma weight residual 113.65 110.51 3.14 1.47e+00 4.63e-01 4.56e+00 ... (remaining 6831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.46: 2789 23.46 - 46.93: 196 46.93 - 70.39: 26 70.39 - 93.85: 9 93.85 - 117.31: 7 Dihedral angle restraints: 3027 sinusoidal: 1260 harmonic: 1767 Sorted by residual: dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 134.03 -41.03 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CA ALA A 177 " pdb=" C ALA A 177 " pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C2 NAG A 503 " pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " pdb=" C5 NAG A 503 " ideal model delta sinusoidal sigma weight residual -62.96 54.35 -117.31 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 3024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 754 0.126 - 0.252: 5 0.252 - 0.378: 1 0.378 - 0.504: 0 0.504 - 0.630: 1 Chirality restraints: 761 Sorted by residual: chirality pdb=" C1 NAG A 503 " pdb=" ND2 ASN A 329 " pdb=" C2 NAG A 503 " pdb=" O5 NAG A 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.93e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ILE A 392 " pdb=" N ILE A 392 " pdb=" C ILE A 392 " pdb=" CB ILE A 392 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 758 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " -0.121 2.00e-02 2.50e+03 1.70e-01 3.63e+02 pdb=" CG ASN A 329 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " -0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " 0.299 2.00e-02 2.50e+03 pdb=" C1 NAG A 503 " -0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 125 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.06e+00 pdb=" N PRO A 126 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 94 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.61e+00 pdb=" N PRO L 95 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.017 5.00e-02 4.00e+02 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 325 2.73 - 3.27: 4643 3.27 - 3.81: 8984 3.81 - 4.36: 11401 4.36 - 4.90: 19097 Nonbonded interactions: 44450 Sorted by model distance: nonbonded pdb=" OG SER A 179 " pdb=" OE2 GLU A 227 " model vdw 2.185 2.440 nonbonded pdb=" OG SER L 27A" pdb=" O ASP A 309 " model vdw 2.243 2.440 nonbonded pdb=" OD1 ASP A 309 " pdb=" OG SER A 311 " model vdw 2.259 2.440 nonbonded pdb=" OD1 ASP A 399 " pdb=" OG SER A 457 " model vdw 2.259 2.440 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.290 2.440 ... (remaining 44445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.34 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: 3.600 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: 10.070 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.820 Find NCS groups from input model: 0.140 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:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 : 0.004 0.085 5038 Z= 0.270 Angle : 0.611 7.172 6836 Z= 0.311 Chirality : 0.051 0.630 761 Planarity : 0.004 0.044 876 Dihedral : 17.343 117.313 1874 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.32 % Allowed : 16.76 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.10 (0.34), residues: 618 helix: 0.60 (2.68), residues: 6 sheet: -0.05 (0.32), residues: 249 loop : 0.04 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.013 0.002 TYR A 121 ARG 0.002 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.576 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 81 average time/residue: 1.0859 time to fit residues: 92.3136 Evaluate side-chains 78 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.605 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.7690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN A 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5038 Z= 0.243 Angle : 0.587 8.693 6836 Z= 0.310 Chirality : 0.048 0.396 761 Planarity : 0.004 0.044 876 Dihedral : 11.895 104.828 788 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.39 % Allowed : 15.82 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.17 (0.33), residues: 618 helix: 0.45 (2.56), residues: 6 sheet: -0.08 (0.32), residues: 233 loop : -0.05 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.012 0.002 PHE A 354 TYR 0.013 0.002 TYR A 121 ARG 0.002 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.590 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 78 average time/residue: 1.0892 time to fit residues: 89.0885 Evaluate side-chains 75 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.580 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.7429 time to fit residues: 3.9086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN A 391 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5038 Z= 0.224 Angle : 0.567 8.821 6836 Z= 0.300 Chirality : 0.047 0.376 761 Planarity : 0.004 0.046 876 Dihedral : 9.558 102.738 788 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.39 % Allowed : 16.38 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.14 (0.33), residues: 618 helix: 0.40 (2.53), residues: 6 sheet: -0.00 (0.32), residues: 232 loop : -0.06 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.013 0.002 TYR A 121 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 0.577 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 82 average time/residue: 1.0735 time to fit residues: 92.2323 Evaluate side-chains 82 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.520 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.6760 time to fit residues: 4.2869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5038 Z= 0.253 Angle : 0.577 9.049 6836 Z= 0.306 Chirality : 0.048 0.400 761 Planarity : 0.004 0.046 876 Dihedral : 9.047 101.179 788 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.14 % Allowed : 16.01 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.17 (0.33), residues: 618 helix: 0.39 (2.53), residues: 6 sheet: -0.04 (0.32), residues: 232 loop : -0.08 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.014 0.002 PHE A 354 TYR 0.013 0.002 TYR A 121 ARG 0.002 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 69 time to evaluate : 0.777 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 83 average time/residue: 1.0523 time to fit residues: 91.5783 Evaluate side-chains 82 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 5 average time/residue: 0.7182 time to fit residues: 4.6086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.0010 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5038 Z= 0.263 Angle : 0.576 9.157 6836 Z= 0.307 Chirality : 0.048 0.401 761 Planarity : 0.004 0.047 876 Dihedral : 8.947 100.282 788 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.01 % Allowed : 17.51 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.20 (0.33), residues: 618 helix: 0.40 (2.55), residues: 6 sheet: -0.05 (0.32), residues: 230 loop : -0.10 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.014 0.002 PHE A 354 TYR 0.013 0.002 TYR A 121 ARG 0.002 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.585 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 81 average time/residue: 1.1857 time to fit residues: 100.7833 Evaluate side-chains 79 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.539 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.5360 time to fit residues: 3.0471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5038 Z= 0.301 Angle : 0.595 9.217 6836 Z= 0.318 Chirality : 0.049 0.405 761 Planarity : 0.004 0.047 876 Dihedral : 8.962 99.850 788 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.14 % Allowed : 16.76 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.22 (0.33), residues: 618 helix: 0.34 (2.52), residues: 6 sheet: -0.07 (0.31), residues: 230 loop : -0.11 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.014 0.002 PHE A 354 TYR 0.015 0.002 TYR L 91 ARG 0.003 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 71 time to evaluate : 0.591 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 86 average time/residue: 1.1001 time to fit residues: 99.0560 Evaluate side-chains 86 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 0.589 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 0.7152 time to fit residues: 4.5746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 0.0050 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5038 Z= 0.178 Angle : 0.545 9.372 6836 Z= 0.288 Chirality : 0.046 0.399 761 Planarity : 0.004 0.047 876 Dihedral : 8.696 98.502 788 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.39 % Allowed : 18.08 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.17 (0.34), residues: 618 helix: 0.39 (2.52), residues: 6 sheet: -0.06 (0.31), residues: 237 loop : -0.05 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 178 HIS 0.002 0.001 HIS A 274 PHE 0.013 0.001 PHE A 354 TYR 0.011 0.001 TYR A 121 ARG 0.001 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.591 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 87 average time/residue: 1.0649 time to fit residues: 97.1139 Evaluate side-chains 83 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.1488 time to fit residues: 1.1187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 53 optimal weight: 0.2980 chunk 56 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5038 Z= 0.251 Angle : 0.575 9.410 6836 Z= 0.305 Chirality : 0.048 0.402 761 Planarity : 0.004 0.047 876 Dihedral : 8.763 98.200 788 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.64 % Allowed : 19.59 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.14 (0.33), residues: 618 helix: 0.35 (2.51), residues: 6 sheet: 0.01 (0.32), residues: 230 loop : -0.07 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.014 0.002 TYR L 91 ARG 0.002 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.583 Fit side-chains outliers start: 14 outliers final: 14 residues processed: 86 average time/residue: 1.0878 time to fit residues: 98.0787 Evaluate side-chains 90 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.578 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.4964 time to fit residues: 2.9204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5038 Z= 0.245 Angle : 0.573 9.490 6836 Z= 0.304 Chirality : 0.048 0.402 761 Planarity : 0.004 0.047 876 Dihedral : 8.735 97.686 788 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.64 % Allowed : 19.40 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.17 (0.33), residues: 618 helix: 0.39 (2.52), residues: 6 sheet: -0.01 (0.32), residues: 225 loop : -0.10 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.014 0.002 TYR L 91 ARG 0.002 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.533 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 86 average time/residue: 1.0941 time to fit residues: 98.5362 Evaluate side-chains 86 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.8391 time to fit residues: 2.4781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.0870 chunk 48 optimal weight: 8.9990 chunk 5 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.0470 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5038 Z= 0.146 Angle : 0.529 9.732 6836 Z= 0.277 Chirality : 0.046 0.393 761 Planarity : 0.004 0.046 876 Dihedral : 8.437 95.582 788 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.45 % Allowed : 20.34 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.13 (0.34), residues: 618 helix: 0.49 (2.50), residues: 6 sheet: -0.01 (0.32), residues: 232 loop : -0.05 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS A 274 PHE 0.012 0.001 PHE A 354 TYR 0.009 0.001 TYR A 121 ARG 0.002 0.000 ARG A 400 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.586 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 87 average time/residue: 1.0376 time to fit residues: 94.7755 Evaluate side-chains 80 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.436 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0771 time to fit residues: 0.7421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.138786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.108637 restraints weight = 4744.464| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.39 r_work: 0.3010 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5038 Z= 0.207 Angle : 0.556 9.783 6836 Z= 0.292 Chirality : 0.047 0.399 761 Planarity : 0.004 0.047 876 Dihedral : 8.469 94.985 788 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.07 % Allowed : 20.90 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.03 (0.34), residues: 618 helix: 0.48 (2.48), residues: 6 sheet: 0.15 (0.33), residues: 225 loop : -0.05 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.012 0.002 TYR A 121 ARG 0.001 0.000 ARG A 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2456.15 seconds wall clock time: 44 minutes 20.13 seconds (2660.13 seconds total)