Starting phenix.real_space_refine on Sun Mar 10 18:58:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/03_2024/7zyl_15026_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/03_2024/7zyl_15026.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/03_2024/7zyl_15026_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/03_2024/7zyl_15026_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/03_2024/7zyl_15026_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/03_2024/7zyl_15026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/03_2024/7zyl_15026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/03_2024/7zyl_15026_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyl_15026/03_2024/7zyl_15026_trim_updated.pdb" } resolution = 2.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2504 2.51 5 N 684 2.21 5 O 784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 133": "OD1" <-> "OD2" Residue "B ASP 133": "OD1" <-> "OD2" Residue "C ASP 133": "OD1" <-> "OD2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D ASP 133": "OD1" <-> "OD2" 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: 3992 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'KFL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'KFL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'KFL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'KFL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.63, per 1000 atoms: 0.66 Number of scatterers: 3992 At special positions: 0 Unit cell: (62.55, 72.45, 66.15, 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 20 16.00 O 784 8.00 N 684 7.00 C 2504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 107 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 107 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 107 " 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 41 " " NAG F 1 " - " ASN B 41 " " NAG G 1 " - " ASN C 41 " " NAG H 1 " - " ASN D 41 " Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 658.0 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 872 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 7 helices and 4 sheets defined 6.8% alpha, 45.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 130 through 135 removed outlier: 4.617A pdb=" N TRP A 134 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 130 through 135 removed outlier: 4.599A pdb=" N TRP B 134 " --> pdb=" O GLY B 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 130 through 135 removed outlier: 4.597A pdb=" N TRP C 134 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 135 removed outlier: 4.602A pdb=" N TRP D 134 " --> pdb=" O GLY D 131 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 41 through 44 removed outlier: 4.410A pdb=" N ARG A 146 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLU A 115 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 41 through 44 removed outlier: 4.419A pdb=" N ARG B 146 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLU B 115 " --> pdb=" O ARG B 146 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 41 through 44 removed outlier: 4.291A pdb=" N ARG C 146 " --> pdb=" O GLU C 115 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLU C 115 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 41 through 44 removed outlier: 4.419A pdb=" N ARG D 146 " --> pdb=" O GLU D 115 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLU D 115 " --> pdb=" O ARG D 146 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 492 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: 1.17 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 636 1.30 - 1.43: 1052 1.43 - 1.56: 2340 1.56 - 1.68: 16 1.68 - 1.81: 28 Bond restraints: 4072 Sorted by residual: bond pdb=" N27 KFL B 201 " pdb=" O28 KFL B 201 " ideal model delta sigma weight residual 1.404 1.171 0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" N27 KFL A 201 " pdb=" O28 KFL A 201 " ideal model delta sigma weight residual 1.404 1.172 0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" N27 KFL D 201 " pdb=" O28 KFL D 201 " ideal model delta sigma weight residual 1.404 1.173 0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" N27 KFL C 201 " pdb=" O28 KFL C 201 " ideal model delta sigma weight residual 1.404 1.173 0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C02 KFL D 201 " pdb=" N27 KFL D 201 " ideal model delta sigma weight residual 1.494 1.439 0.055 2.00e-02 2.50e+03 7.52e+00 ... (remaining 4067 not shown) Histogram of bond angle deviations from ideal: 100.77 - 107.42: 154 107.42 - 114.07: 2456 114.07 - 120.72: 1362 120.72 - 127.37: 1520 127.37 - 134.02: 44 Bond angle restraints: 5536 Sorted by residual: angle pdb=" N ASN D 41 " pdb=" CA ASN D 41 " pdb=" C ASN D 41 " ideal model delta sigma weight residual 110.52 107.14 3.38 1.48e+00 4.57e-01 5.21e+00 angle pdb=" N ASN A 81 " pdb=" CA ASN A 81 " pdb=" CB ASN A 81 " ideal model delta sigma weight residual 113.65 110.31 3.34 1.47e+00 4.63e-01 5.15e+00 angle pdb=" N ILE A 68 " pdb=" CA ILE A 68 " pdb=" CB ILE A 68 " ideal model delta sigma weight residual 110.13 113.67 -3.54 1.56e+00 4.11e-01 5.14e+00 angle pdb=" N ASN A 41 " pdb=" CA ASN A 41 " pdb=" C ASN A 41 " ideal model delta sigma weight residual 110.32 106.79 3.53 1.59e+00 3.96e-01 4.93e+00 angle pdb=" N ASN B 41 " pdb=" CA ASN B 41 " pdb=" C ASN B 41 " ideal model delta sigma weight residual 110.32 106.86 3.46 1.59e+00 3.96e-01 4.72e+00 ... (remaining 5531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 2167 17.77 - 35.54: 215 35.54 - 53.31: 54 53.31 - 71.08: 24 71.08 - 88.84: 20 Dihedral angle restraints: 2480 sinusoidal: 1124 harmonic: 1356 Sorted by residual: dihedral pdb=" CB GLU C 115 " pdb=" CG GLU C 115 " pdb=" CD GLU C 115 " pdb=" OE1 GLU C 115 " ideal model delta sinusoidal sigma weight residual 0.00 -88.84 88.84 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" C04 KFL C 201 " pdb=" C05 KFL C 201 " pdb=" C23 KFL C 201 " pdb=" C24 KFL C 201 " ideal model delta sinusoidal sigma weight residual 52.89 -35.35 88.24 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" C04 KFL B 201 " pdb=" C05 KFL B 201 " pdb=" C23 KFL B 201 " pdb=" C24 KFL B 201 " ideal model delta sinusoidal sigma weight residual 52.89 -35.32 88.21 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 2477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 543 0.055 - 0.110: 94 0.110 - 0.165: 11 0.165 - 0.221: 0 0.221 - 0.276: 8 Chirality restraints: 656 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN C 41 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN D 41 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 41 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 653 not shown) Planarity restraints: 676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 41 " 0.027 2.00e-02 2.50e+03 2.46e-02 7.55e+00 pdb=" CG ASN C 41 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN C 41 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 41 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 41 " -0.026 2.00e-02 2.50e+03 2.38e-02 7.10e+00 pdb=" CG ASN A 41 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 41 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 41 " 0.026 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 41 " -0.026 2.00e-02 2.50e+03 2.37e-02 7.01e+00 pdb=" CG ASN D 41 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN D 41 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D 41 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.026 2.00e-02 2.50e+03 ... (remaining 673 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 79 2.66 - 3.22: 3658 3.22 - 3.78: 6728 3.78 - 4.34: 9635 4.34 - 4.90: 15038 Nonbonded interactions: 35138 Sorted by model distance: nonbonded pdb=" OE2 GLU C 98 " pdb=" ND2 ASN D 81 " model vdw 2.104 2.520 nonbonded pdb=" OG SER C 40 " pdb=" O20 KFL C 201 " model vdw 2.329 2.440 nonbonded pdb=" OG SER B 40 " pdb=" O20 KFL B 201 " model vdw 2.337 2.440 nonbonded pdb=" OG SER A 40 " pdb=" O20 KFL A 201 " model vdw 2.338 2.440 nonbonded pdb=" OG SER D 40 " pdb=" O20 KFL D 201 " model vdw 2.338 2.440 ... (remaining 35133 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 3.650 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: 11.260 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.450 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:14.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 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 : 0.010 0.233 4072 Z= 0.566 Angle : 0.623 5.498 5536 Z= 0.312 Chirality : 0.052 0.276 656 Planarity : 0.003 0.024 672 Dihedral : 18.173 88.845 1596 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.00 % Allowed : 22.14 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.36), residues: 476 helix: -4.93 (0.17), residues: 24 sheet: 0.53 (0.26), residues: 288 loop : 1.26 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 94 HIS 0.001 0.000 HIS B 74 PHE 0.015 0.002 PHE B 90 TYR 0.006 0.002 TYR C 57 ARG 0.002 0.001 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7153 (pm20) REVERT: C 114 LYS cc_start: 0.7508 (mmmt) cc_final: 0.6839 (mmmt) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 1.4692 time to fit residues: 102.8141 Evaluate side-chains 66 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.8781 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 4072 Z= 0.290 Angle : 0.703 6.104 5536 Z= 0.358 Chirality : 0.047 0.126 656 Planarity : 0.004 0.031 672 Dihedral : 15.717 86.685 752 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 3.33 % Allowed : 18.81 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.36), residues: 476 helix: -4.92 (0.18), residues: 24 sheet: 0.45 (0.27), residues: 288 loop : 1.32 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 121 HIS 0.001 0.000 HIS C 74 PHE 0.016 0.002 PHE D 90 TYR 0.006 0.002 TYR B 57 ARG 0.003 0.001 ARG D 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.436 Fit side-chains REVERT: B 67 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6695 (pm20) REVERT: C 67 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6666 (pm20) REVERT: C 114 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6840 (mmmt) outliers start: 14 outliers final: 4 residues processed: 78 average time/residue: 1.2532 time to fit residues: 100.6168 Evaluate side-chains 77 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 4072 Z= 0.188 Angle : 0.654 5.712 5536 Z= 0.327 Chirality : 0.045 0.121 656 Planarity : 0.003 0.021 672 Dihedral : 15.044 86.683 752 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.95 % Allowed : 21.90 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.37), residues: 476 helix: -4.86 (0.18), residues: 24 sheet: 0.34 (0.27), residues: 292 loop : 1.32 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 121 HIS 0.001 0.000 HIS C 74 PHE 0.013 0.002 PHE D 90 TYR 0.006 0.002 TYR B 57 ARG 0.002 0.001 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.466 Fit side-chains REVERT: B 67 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6723 (pm20) REVERT: C 67 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6705 (pm20) REVERT: C 114 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6897 (mmmt) REVERT: D 114 LYS cc_start: 0.7487 (ptmm) cc_final: 0.7031 (ptmm) outliers start: 4 outliers final: 0 residues processed: 72 average time/residue: 1.4929 time to fit residues: 110.5114 Evaluate side-chains 69 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 114 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 0.0170 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 26 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- 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: 0.8761 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 4072 Z= 0.207 Angle : 0.647 5.690 5536 Z= 0.324 Chirality : 0.045 0.120 656 Planarity : 0.004 0.023 672 Dihedral : 15.099 87.510 752 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.86 % Allowed : 20.00 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.37), residues: 476 helix: -4.85 (0.18), residues: 24 sheet: 0.36 (0.27), residues: 292 loop : 1.27 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 121 HIS 0.000 0.000 HIS C 74 PHE 0.015 0.002 PHE D 90 TYR 0.006 0.002 TYR D 57 ARG 0.002 0.001 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6728 (pm20) REVERT: C 67 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6701 (pm20) REVERT: C 114 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6877 (mmmt) outliers start: 12 outliers final: 4 residues processed: 74 average time/residue: 1.3673 time to fit residues: 104.1794 Evaluate side-chains 72 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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: 0.8764 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 4072 Z= 0.228 Angle : 0.664 5.697 5536 Z= 0.333 Chirality : 0.046 0.122 656 Planarity : 0.004 0.023 672 Dihedral : 15.255 88.434 752 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.67 % Allowed : 21.19 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.37), residues: 476 helix: -4.85 (0.18), residues: 24 sheet: 0.35 (0.27), residues: 292 loop : 1.24 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 121 HIS 0.000 0.000 HIS C 74 PHE 0.017 0.002 PHE C 90 TYR 0.006 0.002 TYR D 57 ARG 0.002 0.000 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.420 Fit side-chains REVERT: B 67 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6727 (pm20) REVERT: C 67 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6713 (pm20) REVERT: C 114 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.6871 (mmmt) REVERT: D 114 LYS cc_start: 0.7435 (ptmm) cc_final: 0.6994 (ptmm) outliers start: 7 outliers final: 3 residues processed: 69 average time/residue: 1.4776 time to fit residues: 104.9165 Evaluate side-chains 72 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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: 0.8774 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 4072 Z= 0.273 Angle : 0.673 5.666 5536 Z= 0.342 Chirality : 0.047 0.123 656 Planarity : 0.004 0.028 672 Dihedral : 15.589 90.017 752 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.90 % Allowed : 22.38 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.36), residues: 476 helix: -4.86 (0.18), residues: 24 sheet: 0.30 (0.27), residues: 292 loop : 1.20 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 94 HIS 0.000 0.000 HIS C 74 PHE 0.018 0.002 PHE C 90 TYR 0.006 0.002 TYR C 57 ARG 0.003 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.7387 (ptmm) cc_final: 0.7001 (ptmm) REVERT: B 67 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6760 (pm20) REVERT: C 67 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6746 (pm20) REVERT: C 114 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6916 (mmmt) REVERT: D 114 LYS cc_start: 0.7404 (ptmm) cc_final: 0.6922 (ptmm) outliers start: 8 outliers final: 3 residues processed: 75 average time/residue: 1.4846 time to fit residues: 114.4758 Evaluate side-chains 74 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.8754 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 4072 Z= 0.175 Angle : 0.633 5.598 5536 Z= 0.313 Chirality : 0.044 0.124 656 Planarity : 0.003 0.021 672 Dihedral : 15.056 89.115 752 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.67 % Allowed : 22.86 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.36), residues: 476 helix: -4.84 (0.18), residues: 24 sheet: 0.33 (0.27), residues: 292 loop : 1.25 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 121 HIS 0.001 0.000 HIS C 74 PHE 0.014 0.002 PHE C 90 TYR 0.006 0.001 TYR D 57 ARG 0.002 0.000 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6740 (pm20) REVERT: C 67 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6729 (pm20) REVERT: C 114 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6847 (mtpp) REVERT: D 114 LYS cc_start: 0.7386 (ptmm) cc_final: 0.6952 (ptmm) outliers start: 7 outliers final: 3 residues processed: 71 average time/residue: 1.5268 time to fit residues: 111.3664 Evaluate side-chains 72 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8750 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 4072 Z= 0.167 Angle : 0.623 5.570 5536 Z= 0.308 Chirality : 0.044 0.125 656 Planarity : 0.003 0.021 672 Dihedral : 14.961 89.018 752 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.67 % Allowed : 22.86 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.36), residues: 476 helix: -4.83 (0.18), residues: 24 sheet: 0.34 (0.27), residues: 292 loop : 1.28 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 121 HIS 0.001 0.000 HIS B 74 PHE 0.015 0.002 PHE C 90 TYR 0.005 0.001 TYR A 57 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.470 Fit side-chains REVERT: B 67 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6746 (pm20) REVERT: C 67 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6732 (pm20) REVERT: C 114 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6864 (mtpp) REVERT: D 67 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6703 (pm20) outliers start: 7 outliers final: 3 residues processed: 68 average time/residue: 1.4998 time to fit residues: 104.9179 Evaluate side-chains 73 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.8776 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 4072 Z= 0.282 Angle : 0.682 5.642 5536 Z= 0.344 Chirality : 0.047 0.129 656 Planarity : 0.004 0.030 672 Dihedral : 15.644 90.552 752 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.90 % Allowed : 22.38 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.37), residues: 476 helix: -4.85 (0.18), residues: 24 sheet: 0.33 (0.27), residues: 292 loop : 1.30 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 94 HIS 0.000 0.000 HIS C 74 PHE 0.019 0.002 PHE D 90 TYR 0.006 0.002 TYR B 57 ARG 0.003 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6766 (pm20) REVERT: C 67 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6751 (pm20) REVERT: C 114 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6879 (mmmt) REVERT: D 67 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6720 (pm20) REVERT: D 114 LYS cc_start: 0.7317 (ptmm) cc_final: 0.6893 (ptmm) outliers start: 8 outliers final: 3 residues processed: 67 average time/residue: 1.4680 time to fit residues: 101.2279 Evaluate side-chains 69 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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: 0.8764 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4072 Z= 0.213 Angle : 0.654 5.607 5536 Z= 0.328 Chirality : 0.046 0.158 656 Planarity : 0.004 0.025 672 Dihedral : 15.366 89.806 752 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.67 % Allowed : 22.38 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.36), residues: 476 helix: -4.84 (0.18), residues: 24 sheet: 0.33 (0.27), residues: 292 loop : 1.28 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 121 HIS 0.000 0.000 HIS A 74 PHE 0.017 0.002 PHE B 90 TYR 0.006 0.002 TYR D 57 ARG 0.002 0.000 ARG C 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6770 (pm20) REVERT: C 67 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6752 (pm20) REVERT: C 114 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6846 (mmmt) REVERT: D 67 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6727 (pm20) REVERT: D 114 LYS cc_start: 0.7319 (ptmm) cc_final: 0.6897 (ptmm) outliers start: 7 outliers final: 3 residues processed: 71 average time/residue: 1.4752 time to fit residues: 107.7232 Evaluate side-chains 74 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.122584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.099619 restraints weight = 4605.158| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.29 r_work: 0.3166 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4072 Z= 0.151 Angle : 0.633 5.704 5536 Z= 0.309 Chirality : 0.044 0.149 656 Planarity : 0.003 0.020 672 Dihedral : 14.672 87.716 752 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.43 % Allowed : 23.10 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.36), residues: 476 helix: -4.83 (0.18), residues: 24 sheet: 0.39 (0.27), residues: 292 loop : 1.26 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 121 HIS 0.001 0.000 HIS C 74 PHE 0.014 0.002 PHE B 90 TYR 0.005 0.001 TYR B 57 ARG 0.002 0.000 ARG C 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2403.14 seconds wall clock time: 43 minutes 15.87 seconds (2595.87 seconds total)