Starting phenix.real_space_refine on Sun Mar 10 14:18:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f29_31428/03_2024/7f29_31428_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f29_31428/03_2024/7f29_31428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f29_31428/03_2024/7f29_31428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f29_31428/03_2024/7f29_31428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f29_31428/03_2024/7f29_31428_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f29_31428/03_2024/7f29_31428_updated.pdb" } resolution = 3.1 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= 0.003 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 6 5.16 5 C 1140 2.51 5 N 288 2.21 5 O 360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 11": "OE1" <-> "OE2" Residue "E ASP 23": "OD1" <-> "OD2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "D GLU 11": "OE1" <-> "OE2" Residue "D ASP 23": "OD1" <-> "OD2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F ASP 23": "OD1" <-> "OD2" Residue "A GLU 11": "OE1" <-> "OE2" Residue "A ASP 23": "OD1" <-> "OD2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B ASP 23": "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: 1794 Number of models: 1 Model: "" Number of chains: 18 Chain: "E" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GAL': 1, 'X6X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GAL': 1, 'X6X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GAL': 1, 'X6X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GAL': 1, 'X6X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GAL': 1, 'X6X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GAL': 1, 'X6X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.58, per 1000 atoms: 0.88 Number of scatterers: 1794 At special positions: 0 Unit cell: (56.18, 125.08, 33.92, 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 6 16.00 O 360 8.00 N 288 7.00 C 1140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Links applied BETA1-3 " X6X G 1 " - " GAL G 2 " " X6X H 1 " - " GAL H 2 " " X6X I 1 " - " GAL I 2 " " X6X J 1 " - " GAL J 2 " " X6X K 1 " - " GAL K 2 " " X6X L 1 " - " GAL L 2 " Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 316.9 milliseconds 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 301 1.32 - 1.44: 449 1.44 - 1.56: 1056 1.56 - 1.68: 0 1.68 - 1.80: 12 Bond restraints: 1818 Sorted by residual: bond pdb=" C3 X6X H 1 " pdb=" O3 X6X H 1 " ideal model delta sigma weight residual 1.410 1.511 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C3 X6X K 1 " pdb=" O3 X6X K 1 " ideal model delta sigma weight residual 1.410 1.510 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C3 X6X L 1 " pdb=" O3 X6X L 1 " ideal model delta sigma weight residual 1.410 1.510 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C3 X6X I 1 " pdb=" O3 X6X I 1 " ideal model delta sigma weight residual 1.410 1.510 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C3 X6X G 1 " pdb=" O3 X6X G 1 " ideal model delta sigma weight residual 1.410 1.510 -0.100 2.00e-02 2.50e+03 2.48e+01 ... (remaining 1813 not shown) Histogram of bond angle deviations from ideal: 100.47 - 106.62: 30 106.62 - 112.77: 1072 112.77 - 118.92: 452 118.92 - 125.07: 864 125.07 - 131.22: 18 Bond angle restraints: 2436 Sorted by residual: angle pdb=" C3 GAL I 2 " pdb=" C4 GAL I 2 " pdb=" C5 GAL I 2 " ideal model delta sigma weight residual 107.77 114.51 -6.74 3.00e+00 1.11e-01 5.05e+00 angle pdb=" C3 GAL J 2 " pdb=" C4 GAL J 2 " pdb=" C5 GAL J 2 " ideal model delta sigma weight residual 107.77 114.50 -6.73 3.00e+00 1.11e-01 5.04e+00 angle pdb=" C3 GAL H 2 " pdb=" C4 GAL H 2 " pdb=" C5 GAL H 2 " ideal model delta sigma weight residual 107.77 114.49 -6.72 3.00e+00 1.11e-01 5.01e+00 angle pdb=" C3 GAL K 2 " pdb=" C4 GAL K 2 " pdb=" C5 GAL K 2 " ideal model delta sigma weight residual 107.77 114.48 -6.71 3.00e+00 1.11e-01 5.00e+00 angle pdb=" C3 GAL G 2 " pdb=" C4 GAL G 2 " pdb=" C5 GAL G 2 " ideal model delta sigma weight residual 107.77 114.47 -6.70 3.00e+00 1.11e-01 5.00e+00 ... (remaining 2431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 1046 16.94 - 33.88: 106 33.88 - 50.82: 6 50.82 - 67.76: 6 67.76 - 84.70: 6 Dihedral angle restraints: 1170 sinusoidal: 582 harmonic: 588 Sorted by residual: dihedral pdb=" CB GLU B 22 " pdb=" CG GLU B 22 " pdb=" CD GLU B 22 " pdb=" OE1 GLU B 22 " ideal model delta sinusoidal sigma weight residual 0.00 84.70 -84.70 1 3.00e+01 1.11e-03 9.68e+00 dihedral pdb=" CB GLU C 22 " pdb=" CG GLU C 22 " pdb=" CD GLU C 22 " pdb=" OE1 GLU C 22 " ideal model delta sinusoidal sigma weight residual 0.00 84.70 -84.70 1 3.00e+01 1.11e-03 9.68e+00 dihedral pdb=" CB GLU D 22 " pdb=" CG GLU D 22 " pdb=" CD GLU D 22 " pdb=" OE1 GLU D 22 " ideal model delta sinusoidal sigma weight residual 0.00 84.69 -84.69 1 3.00e+01 1.11e-03 9.68e+00 ... (remaining 1167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 182 0.029 - 0.058: 31 0.058 - 0.087: 22 0.087 - 0.116: 56 0.116 - 0.145: 21 Chirality restraints: 312 Sorted by residual: chirality pdb=" C1 GAL I 2 " pdb=" O3 X6X I 1 " pdb=" C2 GAL I 2 " pdb=" O5 GAL I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.90e+00 chirality pdb=" C1 GAL G 2 " pdb=" O3 X6X G 1 " pdb=" C2 GAL G 2 " pdb=" O5 GAL G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.87e+00 chirality pdb=" C1 GAL J 2 " pdb=" O3 X6X J 1 " pdb=" C2 GAL J 2 " pdb=" O5 GAL J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.53e+00 ... (remaining 309 not shown) Planarity restraints: 288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 20 " -0.008 2.00e-02 2.50e+03 6.37e-03 7.10e-01 pdb=" CG PHE A 20 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 20 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 20 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 20 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 20 " -0.008 2.00e-02 2.50e+03 6.25e-03 6.84e-01 pdb=" CG PHE F 20 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE F 20 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE F 20 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 20 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE F 20 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 20 " -0.008 2.00e-02 2.50e+03 6.20e-03 6.73e-01 pdb=" CG PHE B 20 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 20 " -0.002 2.00e-02 2.50e+03 ... (remaining 285 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 494 2.82 - 3.34: 1468 3.34 - 3.86: 2844 3.86 - 4.38: 2986 4.38 - 4.90: 5936 Nonbonded interactions: 13728 Sorted by model distance: nonbonded pdb=" OE2 GLU A 11 " pdb=" NE2 HIS A 13 " model vdw 2.305 2.520 nonbonded pdb=" OE2 GLU E 11 " pdb=" NE2 HIS E 13 " model vdw 2.305 2.520 nonbonded pdb=" OE2 GLU B 11 " pdb=" NE2 HIS B 13 " model vdw 2.306 2.520 nonbonded pdb=" OE2 GLU D 11 " pdb=" NE2 HIS D 13 " model vdw 2.306 2.520 nonbonded pdb=" OE2 GLU F 11 " pdb=" NE2 HIS F 13 " model vdw 2.306 2.520 ... (remaining 13723 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' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.850 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.430 Find NCS groups from input model: 0.130 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.101 1818 Z= 0.742 Angle : 1.071 6.744 2436 Z= 0.450 Chirality : 0.061 0.145 312 Planarity : 0.002 0.006 288 Dihedral : 14.683 84.703 798 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % 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: -3.96 (0.42), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.32), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 14 PHE 0.014 0.003 PHE A 20 TYR 0.005 0.003 TYR E 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.197 Fit side-chains REVERT: C 11 GLU cc_start: 0.7648 (tt0) cc_final: 0.7422 (tt0) REVERT: D 11 GLU cc_start: 0.7749 (tt0) cc_final: 0.7377 (tt0) REVERT: D 35 MET cc_start: 0.8973 (tpt) cc_final: 0.8732 (tpt) REVERT: B 28 LYS cc_start: 0.9201 (mttp) cc_final: 0.8952 (mttt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1859 time to fit residues: 7.3294 Evaluate side-chains 25 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.0570 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN A 15 GLN B 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1818 Z= 0.137 Angle : 0.555 3.279 2436 Z= 0.272 Chirality : 0.052 0.132 312 Planarity : 0.001 0.006 288 Dihedral : 6.061 20.194 462 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % 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: -3.36 (0.46), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 14 PHE 0.013 0.002 PHE E 20 TYR 0.006 0.002 TYR B 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.173 Fit side-chains REVERT: C 11 GLU cc_start: 0.7713 (tt0) cc_final: 0.7462 (tt0) REVERT: D 11 GLU cc_start: 0.7625 (tt0) cc_final: 0.7317 (tt0) REVERT: D 35 MET cc_start: 0.8893 (tpt) cc_final: 0.8577 (tpt) REVERT: B 13 HIS cc_start: 0.7247 (m-70) cc_final: 0.7029 (m-70) REVERT: B 28 LYS cc_start: 0.9181 (mttp) cc_final: 0.8953 (mttt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1849 time to fit residues: 5.2555 Evaluate side-chains 23 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.0060 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 0.0030 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 1818 Z= 0.110 Angle : 0.462 3.630 2436 Z= 0.237 Chirality : 0.050 0.131 312 Planarity : 0.001 0.007 288 Dihedral : 4.274 14.338 462 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 0.60 % Allowed : 19.05 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.54), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 14 PHE 0.008 0.002 PHE F 20 TYR 0.010 0.003 TYR B 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.194 Fit side-chains REVERT: D 11 GLU cc_start: 0.7644 (tt0) cc_final: 0.7377 (tt0) REVERT: B 16 LYS cc_start: 0.8501 (tttt) cc_final: 0.8272 (ttpt) REVERT: B 28 LYS cc_start: 0.9178 (mttp) cc_final: 0.8939 (mttt) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.2419 time to fit residues: 5.9353 Evaluate side-chains 21 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 0.2980 chunk 17 optimal weight: 0.0000 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.1980 chunk 5 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 HIS E 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1818 Z= 0.167 Angle : 0.477 2.932 2436 Z= 0.249 Chirality : 0.050 0.132 312 Planarity : 0.001 0.006 288 Dihedral : 3.830 13.493 462 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 1.79 % Allowed : 18.45 % Favored : 79.76 % 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: -2.30 (0.56), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 14 PHE 0.011 0.002 PHE E 20 TYR 0.008 0.002 TYR C 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.203 Fit side-chains REVERT: D 11 GLU cc_start: 0.7663 (tt0) cc_final: 0.7396 (tt0) REVERT: B 28 LYS cc_start: 0.9195 (mttp) cc_final: 0.8908 (mttt) outliers start: 3 outliers final: 0 residues processed: 23 average time/residue: 0.2325 time to fit residues: 5.9901 Evaluate side-chains 19 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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: 0.7976 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1818 Z= 0.186 Angle : 0.504 4.333 2436 Z= 0.259 Chirality : 0.050 0.131 312 Planarity : 0.002 0.006 288 Dihedral : 3.711 14.464 462 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 2.38 % Allowed : 18.45 % Favored : 79.17 % 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: -2.18 (0.56), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 14 PHE 0.013 0.002 PHE E 20 TYR 0.010 0.003 TYR B 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.200 Fit side-chains REVERT: D 11 GLU cc_start: 0.7711 (tt0) cc_final: 0.7425 (tt0) REVERT: D 35 MET cc_start: 0.8885 (tpt) cc_final: 0.8583 (tpt) REVERT: B 28 LYS cc_start: 0.9209 (mttp) cc_final: 0.8958 (mtmt) outliers start: 4 outliers final: 0 residues processed: 23 average time/residue: 0.2210 time to fit residues: 5.7443 Evaluate side-chains 20 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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: 0.8023 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 1818 Z= 0.323 Angle : 0.586 5.810 2436 Z= 0.298 Chirality : 0.051 0.133 312 Planarity : 0.002 0.007 288 Dihedral : 3.828 14.723 462 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 0.00 % Allowed : 20.83 % Favored : 79.17 % 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: -2.28 (0.56), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 14 PHE 0.016 0.003 PHE E 20 TYR 0.007 0.003 TYR B 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.199 Fit side-chains REVERT: D 11 GLU cc_start: 0.7722 (tt0) cc_final: 0.7401 (tt0) REVERT: D 35 MET cc_start: 0.8893 (tpt) cc_final: 0.8613 (tpt) REVERT: B 28 LYS cc_start: 0.9216 (mttp) cc_final: 0.8963 (mtmt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2214 time to fit residues: 5.5014 Evaluate side-chains 21 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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: 0.7968 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1818 Z= 0.141 Angle : 0.490 4.830 2436 Z= 0.249 Chirality : 0.050 0.133 312 Planarity : 0.001 0.005 288 Dihedral : 3.573 15.054 462 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 23.21 % Favored : 76.79 % 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: -2.17 (0.56), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 14 PHE 0.012 0.002 PHE F 20 TYR 0.009 0.002 TYR D 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.185 Fit side-chains REVERT: D 11 GLU cc_start: 0.7762 (tt0) cc_final: 0.7451 (tt0) REVERT: B 28 LYS cc_start: 0.9203 (mttp) cc_final: 0.8955 (mtmt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1908 time to fit residues: 4.3173 Evaluate side-chains 20 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.0170 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.8220 ------------------------------------------------------------------------------- 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: 0.7958 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1818 Z= 0.134 Angle : 0.472 5.573 2436 Z= 0.241 Chirality : 0.050 0.134 312 Planarity : 0.001 0.005 288 Dihedral : 3.362 14.240 462 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 24.40 % Favored : 75.60 % 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: -2.07 (0.57), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 13 PHE 0.010 0.002 PHE E 20 TYR 0.005 0.002 TYR F 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.199 Fit side-chains REVERT: D 11 GLU cc_start: 0.7763 (tt0) cc_final: 0.7465 (tt0) REVERT: B 28 LYS cc_start: 0.9197 (mttp) cc_final: 0.8943 (mttt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.2441 time to fit residues: 5.4718 Evaluate side-chains 20 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7951 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1818 Z= 0.133 Angle : 0.478 5.610 2436 Z= 0.243 Chirality : 0.050 0.133 312 Planarity : 0.001 0.006 288 Dihedral : 3.344 14.153 462 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 25.60 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.57), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 14 PHE 0.010 0.002 PHE E 20 TYR 0.010 0.002 TYR D 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.230 Fit side-chains REVERT: D 11 GLU cc_start: 0.7694 (tt0) cc_final: 0.7413 (tt0) REVERT: B 28 LYS cc_start: 0.9197 (mttp) cc_final: 0.8948 (mttt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.2375 time to fit residues: 5.3714 Evaluate side-chains 19 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.7975 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1818 Z= 0.193 Angle : 0.503 6.065 2436 Z= 0.258 Chirality : 0.050 0.134 312 Planarity : 0.001 0.005 288 Dihedral : 3.398 14.037 462 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 26.19 % Favored : 73.81 % 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: -2.03 (0.57), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 14 PHE 0.012 0.002 PHE E 20 TYR 0.006 0.002 TYR B 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.193 Fit side-chains REVERT: D 11 GLU cc_start: 0.7762 (tt0) cc_final: 0.7460 (tt0) REVERT: B 28 LYS cc_start: 0.9204 (mttp) cc_final: 0.8955 (mttt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1945 time to fit residues: 4.4040 Evaluate side-chains 20 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4493 r_free = 0.4493 target = 0.192554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.138693 restraints weight = 1834.696| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.24 r_work: 0.3809 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1818 Z= 0.221 Angle : 0.522 6.475 2436 Z= 0.268 Chirality : 0.050 0.133 312 Planarity : 0.002 0.006 288 Dihedral : 3.500 14.587 462 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 25.60 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.57), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 14 PHE 0.014 0.003 PHE F 20 TYR 0.012 0.003 TYR D 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 955.92 seconds wall clock time: 18 minutes 12.35 seconds (1092.35 seconds total)