Starting phenix.real_space_refine on Sun Mar 10 17:49:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlz_25991/03_2024/7tlz_25991.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlz_25991/03_2024/7tlz_25991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlz_25991/03_2024/7tlz_25991.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlz_25991/03_2024/7tlz_25991.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlz_25991/03_2024/7tlz_25991.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tlz_25991/03_2024/7tlz_25991.pdb" } resolution = 3.3 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= 0.049 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 14 5.16 5 C 2359 2.51 5 N 603 2.21 5 O 645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 237": "NH1" <-> "NH2" Residue "J PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3621 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 761 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1957 Unusual residues: {'NAG': 6} Classifications: {'peptide': 251, 'undetermined': 6} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 15, 'TRANS': 235, None: 6} Not linked: pdbres="PHE J 306 " pdbres="NAG J1401 " Not linked: pdbres="NAG J1401 " pdbres="NAG J1402 " Not linked: pdbres="NAG J1402 " pdbres="NAG J1403 " Not linked: pdbres="NAG J1403 " pdbres="NAG J1404 " Not linked: pdbres="NAG J1404 " pdbres="NAG J1405 " Not linked: pdbres="NAG J1405 " pdbres="NAG J1406 " Chain breaks: 5 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 10, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 90 Time building chain proxies: 2.47, per 1000 atoms: 0.68 Number of scatterers: 3621 At special positions: 0 Unit cell: (84.3, 69.126, 76.713, 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 14 16.00 O 645 8.00 N 603 7.00 C 2359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.20 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 15 " - pdb=" SG CYS J 136 " distance=2.04 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 166 " distance=2.03 Simple disulfide: pdb=" SG CYS J 291 " - pdb=" SG CYS J 301 " distance=2.02 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 NAG-ASN " NAG J1401 " - " ASN J 165 " " NAG J1402 " - " ASN J 282 " " NAG J1403 " - " ASN J 17 " " NAG J1404 " - " ASN J 234 " " NAG J1405 " - " ASN J 61 " " NAG J1406 " - " ASN J 122 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 830.8 milliseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 884 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 11 sheets defined 4.2% alpha, 50.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'J' and resid 294 through 303 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 4.086A pdb=" N ASP A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 67 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 6.651A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 33 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 97 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 6.651A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 33 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.702A pdb=" N MET B 34 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'J' and resid 27 through 30 Processing sheet with id=AA8, first strand: chain 'J' and resid 27 through 30 removed outlier: 8.184A pdb=" N ASN J 61 " --> pdb=" O TYR J 269 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR J 269 " --> pdb=" O ASN J 61 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE J 201 " --> pdb=" O ASP J 228 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP J 228 " --> pdb=" O PHE J 201 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE J 203 " --> pdb=" O LEU J 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 47 through 55 removed outlier: 4.067A pdb=" N ASP J 287 " --> pdb=" O LYS J 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 84 through 85 removed outlier: 13.167A pdb=" N PHE J 238 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 13.074A pdb=" N PHE J 135 " --> pdb=" O PHE J 238 " (cutoff:3.500A) removed outlier: 13.017A pdb=" N THR J 240 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N ASN J 137 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N LEU J 242 " --> pdb=" O ASN J 137 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU J 244 " --> pdb=" O PRO J 139 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU J 141 " --> pdb=" O LEU J 244 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER J 162 " --> pdb=" O GLN J 134 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N CYS J 136 " --> pdb=" O TYR J 160 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR J 160 " --> pdb=" O CYS J 136 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP J 138 " --> pdb=" O ARG J 158 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ARG J 158 " --> pdb=" O ASP J 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 84 through 85 removed outlier: 3.576A pdb=" N GLY J 103 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA J 243 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE J 101 " --> pdb=" O ALA J 243 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ARG J 102 " --> pdb=" O ASN J 121 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE J 168 " --> pdb=" O VAL J 130 " (cutoff:3.500A) 178 hydrogen bonds defined for protein. 423 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: 0.93 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 636 1.32 - 1.45: 1067 1.45 - 1.58: 1993 1.58 - 1.71: 1 1.71 - 1.84: 18 Bond restraints: 3715 Sorted by residual: bond pdb=" CA ASN J 165 " pdb=" C ASN J 165 " ideal model delta sigma weight residual 1.523 1.582 -0.059 1.42e-02 4.96e+03 1.73e+01 bond pdb=" CA CYS J 131 " pdb=" C CYS J 131 " ideal model delta sigma weight residual 1.522 1.567 -0.046 1.24e-02 6.50e+03 1.36e+01 bond pdb=" C ASN J 165 " pdb=" O ASN J 165 " ideal model delta sigma weight residual 1.235 1.195 0.040 1.20e-02 6.94e+03 1.10e+01 bond pdb=" C5 NAG J1406 " pdb=" O5 NAG J1406 " ideal model delta sigma weight residual 1.413 1.473 -0.060 2.00e-02 2.50e+03 9.10e+00 bond pdb=" C5 NAG J1401 " pdb=" O5 NAG J1401 " ideal model delta sigma weight residual 1.413 1.473 -0.060 2.00e-02 2.50e+03 8.89e+00 ... (remaining 3710 not shown) Histogram of bond angle deviations from ideal: 100.80 - 107.40: 133 107.40 - 114.00: 1945 114.00 - 120.59: 1538 120.59 - 127.19: 1419 127.19 - 133.79: 27 Bond angle restraints: 5062 Sorted by residual: angle pdb=" C LEU J 24 " pdb=" N PRO J 25 " pdb=" CA PRO J 25 " ideal model delta sigma weight residual 119.66 125.78 -6.12 7.20e-01 1.93e+00 7.23e+01 angle pdb=" C ASP J 138 " pdb=" N PRO J 139 " pdb=" CA PRO J 139 " ideal model delta sigma weight residual 119.76 127.46 -7.70 1.00e+00 1.00e+00 5.93e+01 angle pdb=" C PRO J 25 " pdb=" N PRO J 26 " pdb=" CA PRO J 26 " ideal model delta sigma weight residual 119.85 127.21 -7.36 1.01e+00 9.80e-01 5.32e+01 angle pdb=" C GLY A 99 " pdb=" N PRO A 100 " pdb=" CA PRO A 100 " ideal model delta sigma weight residual 119.32 127.60 -8.28 1.14e+00 7.69e-01 5.28e+01 angle pdb=" C ASP J 294 " pdb=" N PRO J 295 " pdb=" CA PRO J 295 " ideal model delta sigma weight residual 119.56 126.43 -6.87 1.02e+00 9.61e-01 4.54e+01 ... (remaining 5057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.38: 2120 14.38 - 28.75: 80 28.75 - 43.13: 17 43.13 - 57.51: 6 57.51 - 71.88: 4 Dihedral angle restraints: 2227 sinusoidal: 849 harmonic: 1378 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 50.62 42.38 1 1.00e+01 1.00e-02 2.51e+01 dihedral pdb=" CA TYR B 95 " pdb=" C TYR B 95 " pdb=" N CYS B 96 " pdb=" CA CYS B 96 " ideal model delta harmonic sigma weight residual 180.00 164.28 15.72 0 5.00e+00 4.00e-02 9.88e+00 dihedral pdb=" CG ARG B 67 " pdb=" CD ARG B 67 " pdb=" NE ARG B 67 " pdb=" CZ ARG B 67 " ideal model delta sinusoidal sigma weight residual 180.00 139.40 40.60 2 1.50e+01 4.44e-03 9.03e+00 ... (remaining 2224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 409 0.071 - 0.142: 128 0.142 - 0.212: 24 0.212 - 0.283: 9 0.283 - 0.354: 5 Chirality restraints: 575 Sorted by residual: chirality pdb=" C2 NAG J1405 " pdb=" C1 NAG J1405 " pdb=" C3 NAG J1405 " pdb=" N2 NAG J1405 " both_signs ideal model delta sigma weight residual False -2.49 -2.85 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C2 NAG J1401 " pdb=" C1 NAG J1401 " pdb=" C3 NAG J1401 " pdb=" N2 NAG J1401 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C2 NAG J1403 " pdb=" C1 NAG J1403 " pdb=" C3 NAG J1403 " pdb=" N2 NAG J1403 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 572 not shown) Planarity restraints: 650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN J 282 " 0.026 2.00e-02 2.50e+03 2.85e-02 1.01e+01 pdb=" CG ASN J 282 " -0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN J 282 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN J 282 " -0.045 2.00e-02 2.50e+03 pdb=" C1 NAG J1402 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 269 " 0.033 2.00e-02 2.50e+03 1.66e-02 5.54e+00 pdb=" CG TYR J 269 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR J 269 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR J 269 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR J 269 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR J 269 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR J 269 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR J 269 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 17 " 0.019 2.00e-02 2.50e+03 1.99e-02 4.94e+00 pdb=" CG ASN J 17 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN J 17 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN J 17 " -0.031 2.00e-02 2.50e+03 pdb=" C1 NAG J1403 " 0.024 2.00e-02 2.50e+03 ... (remaining 647 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 2061 3.04 - 3.51: 3034 3.51 - 3.97: 5566 3.97 - 4.44: 6349 4.44 - 4.90: 10682 Nonbonded interactions: 27692 Sorted by model distance: nonbonded pdb=" O ASP A 92 " pdb=" NH1 ARG B 103 " model vdw 2.581 2.520 nonbonded pdb=" C ASP B 101 " pdb=" OD1 ASP B 101 " model vdw 2.611 3.270 nonbonded pdb=" N ASN J 165 " pdb=" OD1 ASN J 165 " model vdw 2.617 2.520 nonbonded pdb=" N LYS B 76 " pdb=" N ASN B 77 " model vdw 2.628 2.560 nonbonded pdb=" N GLY B 33 " pdb=" O GLY B 33 " model vdw 2.641 2.496 ... (remaining 27687 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 27.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.810 Find NCS groups from input model: 0.090 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.011 0.060 3715 Z= 0.704 Angle : 1.301 8.282 5062 Z= 0.878 Chirality : 0.078 0.354 575 Planarity : 0.005 0.021 644 Dihedral : 9.091 71.882 1328 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.31 % Allowed : 0.31 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.02 (0.38), residues: 457 helix: -0.12 (1.59), residues: 11 sheet: 1.60 (0.36), residues: 187 loop : 0.04 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP J 64 HIS 0.002 0.001 HIS B 35 PHE 0.016 0.003 PHE A 98 TYR 0.033 0.005 TYR J 269 ARG 0.004 0.001 ARG J 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 202 LYS cc_start: 0.8602 (mttm) cc_final: 0.8380 (mttp) outliers start: 1 outliers final: 1 residues processed: 84 average time/residue: 0.2404 time to fit residues: 23.4491 Evaluate side-chains 60 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 165 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.0270 chunk 35 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 14 optimal weight: 0.0970 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN B 74 ASN J 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3715 Z= 0.149 Angle : 0.569 10.315 5062 Z= 0.303 Chirality : 0.046 0.192 575 Planarity : 0.004 0.023 644 Dihedral : 4.715 24.793 639 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.31 % Allowed : 5.94 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.95 (0.38), residues: 457 helix: 2.13 (1.55), residues: 11 sheet: 1.51 (0.39), residues: 171 loop : 0.03 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS J 66 PHE 0.014 0.001 PHE J 79 TYR 0.019 0.001 TYR J 265 ARG 0.002 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.413 Fit side-chains REVERT: J 41 LYS cc_start: 0.7387 (mttt) cc_final: 0.6984 (mtpt) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.2205 time to fit residues: 13.9065 Evaluate side-chains 51 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.0070 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3715 Z= 0.247 Angle : 0.582 6.884 5062 Z= 0.304 Chirality : 0.048 0.217 575 Planarity : 0.004 0.028 644 Dihedral : 4.209 23.629 637 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.31 % Allowed : 7.19 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.81 (0.39), residues: 457 helix: 2.27 (1.56), residues: 11 sheet: 1.47 (0.39), residues: 180 loop : -0.19 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.003 0.001 HIS J 66 PHE 0.016 0.002 PHE A 98 TYR 0.021 0.002 TYR J 265 ARG 0.004 0.001 ARG J 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.404 Fit side-chains REVERT: J 41 LYS cc_start: 0.7493 (mttt) cc_final: 0.7091 (mtpt) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.2092 time to fit residues: 13.0321 Evaluate side-chains 50 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 0.0000 chunk 40 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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: 0.8068 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3715 Z= 0.275 Angle : 0.575 6.596 5062 Z= 0.299 Chirality : 0.047 0.204 575 Planarity : 0.004 0.037 644 Dihedral : 4.322 29.907 637 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.31 % Allowed : 9.69 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.96 (0.39), residues: 457 helix: 2.17 (1.68), residues: 11 sheet: 1.79 (0.36), residues: 201 loop : -0.48 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.014 0.002 PHE J 92 TYR 0.018 0.002 TYR J 265 ARG 0.003 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.401 Fit side-chains REVERT: J 205 SER cc_start: 0.9087 (p) cc_final: 0.8790 (t) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.2117 time to fit residues: 13.2057 Evaluate side-chains 49 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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: 0.8130 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 3715 Z= 0.408 Angle : 0.657 7.770 5062 Z= 0.338 Chirality : 0.050 0.212 575 Planarity : 0.005 0.032 644 Dihedral : 4.879 41.340 637 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.62 % Allowed : 9.38 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.55 (0.39), residues: 457 helix: 1.83 (1.80), residues: 11 sheet: 1.69 (0.37), residues: 200 loop : -0.92 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 47 HIS 0.003 0.002 HIS J 143 PHE 0.020 0.002 PHE J 92 TYR 0.024 0.002 TYR J 265 ARG 0.004 0.001 ARG J 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.443 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 0.2185 time to fit residues: 12.3063 Evaluate side-chains 45 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain J residue 227 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 15 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.8071 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3715 Z= 0.181 Angle : 0.521 5.984 5062 Z= 0.271 Chirality : 0.046 0.186 575 Planarity : 0.004 0.028 644 Dihedral : 4.511 41.921 637 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.94 % Allowed : 9.38 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.69 (0.39), residues: 457 helix: 2.11 (1.84), residues: 11 sheet: 1.75 (0.36), residues: 205 loop : -0.85 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.012 0.001 PHE J 92 TYR 0.019 0.001 TYR J 265 ARG 0.002 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.410 Fit side-chains REVERT: J 41 LYS cc_start: 0.7540 (mttt) cc_final: 0.7155 (mtpt) REVERT: J 205 SER cc_start: 0.9057 (p) cc_final: 0.8780 (t) outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 0.2148 time to fit residues: 13.4395 Evaluate side-chains 49 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain J residue 227 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 overall best weight: 0.8166 ------------------------------------------------------------------------------- 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: 0.8109 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3715 Z= 0.295 Angle : 0.583 6.713 5062 Z= 0.301 Chirality : 0.048 0.200 575 Planarity : 0.004 0.031 644 Dihedral : 4.747 43.717 637 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.62 % Allowed : 9.69 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.50 (0.38), residues: 457 helix: 1.93 (1.85), residues: 11 sheet: 1.69 (0.36), residues: 204 loop : -1.05 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.016 0.002 PHE J 92 TYR 0.024 0.002 TYR J 265 ARG 0.002 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.410 Fit side-chains REVERT: J 41 LYS cc_start: 0.7575 (mttt) cc_final: 0.7169 (mtpt) REVERT: J 205 SER cc_start: 0.9077 (p) cc_final: 0.8745 (t) REVERT: J 304 LYS cc_start: 0.8559 (mmtm) cc_final: 0.8137 (mptt) outliers start: 2 outliers final: 2 residues processed: 49 average time/residue: 0.2250 time to fit residues: 13.1415 Evaluate side-chains 50 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain J residue 227 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 41 optimal weight: 0.0270 chunk 43 optimal weight: 0.0970 chunk 39 optimal weight: 0.1980 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3715 Z= 0.155 Angle : 0.502 5.912 5062 Z= 0.261 Chirality : 0.045 0.185 575 Planarity : 0.003 0.026 644 Dihedral : 4.430 41.709 637 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.62 % Allowed : 9.69 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.71 (0.39), residues: 457 helix: 2.24 (1.84), residues: 11 sheet: 1.84 (0.37), residues: 196 loop : -0.81 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.011 0.001 PHE J 92 TYR 0.019 0.001 TYR J 265 ARG 0.001 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.366 Fit side-chains REVERT: J 41 LYS cc_start: 0.7518 (mttt) cc_final: 0.7087 (mtpt) REVERT: J 205 SER cc_start: 0.9028 (p) cc_final: 0.8778 (t) outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 0.2254 time to fit residues: 12.8706 Evaluate side-chains 48 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.0060 chunk 42 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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: 0.8073 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3715 Z= 0.198 Angle : 0.521 6.138 5062 Z= 0.269 Chirality : 0.046 0.192 575 Planarity : 0.004 0.030 644 Dihedral : 4.392 41.179 637 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.62 % Allowed : 10.00 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.68 (0.38), residues: 457 helix: 2.23 (1.82), residues: 11 sheet: 1.85 (0.36), residues: 194 loop : -0.85 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.012 0.001 PHE J 92 TYR 0.020 0.001 TYR J 265 ARG 0.001 0.000 ARG J 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.419 Fit side-chains REVERT: J 41 LYS cc_start: 0.7513 (mttt) cc_final: 0.7103 (mtpt) REVERT: J 205 SER cc_start: 0.9041 (p) cc_final: 0.8776 (t) outliers start: 2 outliers final: 2 residues processed: 49 average time/residue: 0.2211 time to fit residues: 12.9407 Evaluate side-chains 49 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 105 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.0170 chunk 5 optimal weight: 0.3980 chunk 10 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 overall best weight: 0.3218 ------------------------------------------------------------------------------- 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: 0.8045 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3715 Z= 0.141 Angle : 0.488 5.830 5062 Z= 0.252 Chirality : 0.045 0.186 575 Planarity : 0.003 0.027 644 Dihedral : 4.185 39.034 637 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.62 % Allowed : 10.00 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.78 (0.39), residues: 457 helix: 2.40 (1.79), residues: 11 sheet: 1.83 (0.37), residues: 196 loop : -0.72 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.003 0.001 HIS B 35 PHE 0.010 0.001 PHE J 92 TYR 0.020 0.001 TYR J 265 ARG 0.001 0.000 ARG A 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.441 Fit side-chains REVERT: B 80 TYR cc_start: 0.8354 (m-80) cc_final: 0.8010 (m-80) REVERT: J 41 LYS cc_start: 0.7461 (mttt) cc_final: 0.7006 (mtpt) REVERT: J 205 SER cc_start: 0.9020 (p) cc_final: 0.8775 (t) outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.2216 time to fit residues: 13.2901 Evaluate side-chains 47 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 105 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.143564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.113259 restraints weight = 4587.093| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.87 r_work: 0.3059 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 3715 Z= 0.346 Angle : 0.607 7.331 5062 Z= 0.312 Chirality : 0.049 0.209 575 Planarity : 0.004 0.034 644 Dihedral : 4.733 42.230 637 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.94 % Allowed : 9.38 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.55 (0.39), residues: 457 helix: 2.09 (1.83), residues: 11 sheet: 1.75 (0.36), residues: 195 loop : -0.92 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 47 HIS 0.004 0.002 HIS B 35 PHE 0.017 0.002 PHE J 92 TYR 0.025 0.002 TYR J 265 ARG 0.002 0.001 ARG J 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1563.67 seconds wall clock time: 28 minutes 45.22 seconds (1725.22 seconds total)