Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:36:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f29_31428/11_2022/7f29_31428_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f29_31428/11_2022/7f29_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_31428/11_2022/7f29_31428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f29_31428/11_2022/7f29_31428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f29_31428/11_2022/7f29_31428_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f29_31428/11_2022/7f29_31428_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4778/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: 1 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: 1 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: 1 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: 1 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: 1 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: 1 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: 1.49, per 1000 atoms: 0.83 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: 1.01 Conformation dependent library (CDL) restraints added in 254.8 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: 0.12 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: 1.04 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=" C1 X6X G 1 " pdb=" O1 X6X G 1 " ideal model delta sigma weight residual 1.291 1.372 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 X6X J 1 " pdb=" O1 X6X J 1 " ideal model delta sigma weight residual 1.291 1.372 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 X6X I 1 " pdb=" O1 X6X I 1 " ideal model delta sigma weight residual 1.291 1.372 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 X6X L 1 " pdb=" O1 X6X L 1 " ideal model delta sigma weight residual 1.291 1.372 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 X6X H 1 " pdb=" O1 X6X H 1 " ideal model delta sigma weight residual 1.291 1.372 -0.081 2.00e-02 2.50e+03 1.63e+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=" C4 GAL G 2 " pdb=" C5 GAL G 2 " pdb=" C6 GAL G 2 " ideal model delta sigma weight residual 114.19 108.94 5.25 2.42e+00 1.70e-01 4.68e+00 angle pdb=" C4 GAL K 2 " pdb=" C5 GAL K 2 " pdb=" C6 GAL K 2 " ideal model delta sigma weight residual 114.19 108.98 5.21 2.42e+00 1.70e-01 4.62e+00 angle pdb=" C4 GAL H 2 " pdb=" C5 GAL H 2 " pdb=" C6 GAL H 2 " ideal model delta sigma weight residual 114.19 109.00 5.19 2.42e+00 1.70e-01 4.59e+00 angle pdb=" C4 GAL L 2 " pdb=" C5 GAL L 2 " pdb=" C6 GAL L 2 " ideal model delta sigma weight residual 114.19 109.00 5.19 2.42e+00 1.70e-01 4.58e+00 angle pdb=" C4 GAL J 2 " pdb=" C5 GAL J 2 " pdb=" C6 GAL J 2 " ideal model delta sigma weight residual 114.19 109.00 5.19 2.42e+00 1.70e-01 4.57e+00 ... (remaining 2431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 900 16.94 - 33.88: 66 33.88 - 50.82: 6 50.82 - 67.76: 6 67.76 - 84.70: 6 Dihedral angle restraints: 984 sinusoidal: 396 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 981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 163 0.031 - 0.061: 52 0.061 - 0.092: 40 0.092 - 0.122: 39 0.122 - 0.153: 18 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 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. 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: 0.320 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: 1.860 Check model and map are aligned: 0.030 Convert atoms to be neutral: 0.020 Process input model: 10.250 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 : 0.012 0.081 1818 Z= 0.614 Angle : 0.909 5.248 2436 Z= 0.429 Chirality : 0.062 0.153 312 Planarity : 0.002 0.006 288 Dihedral : 15.085 84.703 612 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 0.190 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1710 time to fit residues: 6.7470 Evaluate side-chains 25 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.189 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2319 ------------------------------------------------------------------------------- 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: 1.9990 chunk 8 optimal weight: 0.0270 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 1818 Z= 0.152 Angle : 0.522 3.020 2436 Z= 0.265 Chirality : 0.051 0.133 312 Planarity : 0.001 0.006 288 Dihedral : 4.659 16.005 276 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer Outliers : 0.60 % 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: -3.32 (0.46), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.35), residues: 210 *********************** 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: 1 poor density : 24 time to evaluate : 0.192 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.2070 time to fit residues: 5.6163 Evaluate side-chains 22 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.200 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2539 ------------------------------------------------------------------------------- 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: 0.5980 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.0470 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.013 1818 Z= 0.138 Angle : 0.481 3.268 2436 Z= 0.249 Chirality : 0.050 0.132 312 Planarity : 0.001 0.006 288 Dihedral : 4.202 14.746 276 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer Outliers : 0.00 % 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: -2.67 (0.52), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.40), residues: 210 *********************** 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 21 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.201 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.2466 time to fit residues: 5.7874 Evaluate side-chains 20 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.204 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2518 ------------------------------------------------------------------------------- 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: 0.4980 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 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: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.023 1818 Z= 0.348 Angle : 0.584 4.027 2436 Z= 0.306 Chirality : 0.051 0.129 312 Planarity : 0.002 0.007 288 Dihedral : 4.495 15.078 276 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.81 % Favored : 86.19 % Rotamer Outliers : 0.00 % 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 : -1.91 (0.41), residues: 210 *********************** 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 21 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.198 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.2236 time to fit residues: 5.3063 Evaluate side-chains 21 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.205 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2593 ------------------------------------------------------------------------------- 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: 8.9990 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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: 0.8262 moved from start: 0.1595 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= 0.217 Angle : 0.497 3.494 2436 Z= 0.262 Chirality : 0.050 0.132 312 Planarity : 0.002 0.006 288 Dihedral : 4.326 15.326 276 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer Outliers : 3.57 % 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: -2.40 (0.55), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.42), residues: 210 *********************** 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 25 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.196 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 25 average time/residue: 0.1960 time to fit residues: 5.5578 Evaluate side-chains 20 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.194 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2465 ------------------------------------------------------------------------------- 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: 0.9990 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: 1.9990 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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: 0.8284 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.018 1818 Z= 0.273 Angle : 0.570 5.480 2436 Z= 0.289 Chirality : 0.050 0.131 312 Planarity : 0.002 0.006 288 Dihedral : 4.342 14.954 276 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer Outliers : 1.19 % 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: -2.40 (0.55), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.42), residues: 210 *********************** 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 23 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.199 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 23 average time/residue: 0.2324 time to fit residues: 6.1204 Evaluate side-chains 21 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.254 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4717 ------------------------------------------------------------------------------- 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: 2.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8249 moved from start: 0.1866 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= 0.164 Angle : 0.509 4.991 2436 Z= 0.257 Chirality : 0.050 0.134 312 Planarity : 0.001 0.006 288 Dihedral : 4.209 15.056 276 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer Outliers : 0.00 % 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: -2.27 (0.56), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.43), residues: 210 *********************** 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 19 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.196 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2254 time to fit residues: 4.8511 Evaluate side-chains 19 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.196 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2519 ------------------------------------------------------------------------------- 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: 4.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.8239 moved from start: 0.1980 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= 0.155 Angle : 0.491 5.690 2436 Z= 0.249 Chirality : 0.050 0.131 312 Planarity : 0.001 0.005 288 Dihedral : 3.985 14.482 276 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer Outliers : 0.60 % 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: -2.18 (0.57), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.43), residues: 210 *********************** 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: 1 poor density : 19 time to evaluate : 0.202 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.2209 time to fit residues: 4.7522 Evaluate side-chains 20 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.198 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2775 time to fit residues: 0.5412 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8223 moved from start: 0.2039 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= 0.136 Angle : 0.486 5.666 2436 Z= 0.245 Chirality : 0.050 0.132 312 Planarity : 0.001 0.005 288 Dihedral : 3.977 14.375 276 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer Outliers : 0.00 % 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: -2.11 (0.57), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.44), residues: 210 *********************** 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 19 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.209 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2488 time to fit residues: 5.4027 Evaluate side-chains 19 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.303 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3416 ------------------------------------------------------------------------------- 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: 2.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 0.0270 chunk 0 optimal weight: 9.9990 chunk 3 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.008 1818 Z= 0.106 Angle : 0.458 5.759 2436 Z= 0.232 Chirality : 0.050 0.132 312 Planarity : 0.001 0.004 288 Dihedral : 3.772 14.059 276 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer Outliers : 0.00 % 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: -2.02 (0.58), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.44), residues: 210 ********************** 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 : 0.195 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.2187 time to fit residues: 4.9565 Evaluate side-chains 19 residues out of total 168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.194 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2466 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.4495 r_free = 0.4495 target = 0.194129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.139532 restraints weight = 1829.954| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 3.27 r_work: 0.3942 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3930 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work: 0.3918 rms_B_bonded: 2.95 restraints_weight: 0.1250 r_work: 0.3905 rms_B_bonded: 3.01 restraints_weight: 0.0625 r_work: 0.3891 rms_B_bonded: 3.12 restraints_weight: 0.0312 r_work: 0.3875 rms_B_bonded: 3.26 restraints_weight: 0.0156 r_work: 0.3858 rms_B_bonded: 3.45 restraints_weight: 0.0078 r_work: 0.3838 rms_B_bonded: 3.70 restraints_weight: 0.0039 r_work: 0.3816 rms_B_bonded: 4.01 restraints_weight: 0.0020 r_work: 0.3791 rms_B_bonded: 4.39 restraints_weight: 0.0010 r_work: 0.3763 rms_B_bonded: 4.86 restraints_weight: 0.0005 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.017 1818 Z= 0.241 Angle : 0.528 6.424 2436 Z= 0.270 Chirality : 0.050 0.131 312 Planarity : 0.002 0.006 288 Dihedral : 4.006 13.893 276 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer Outliers : 0.00 % 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: -2.02 (0.58), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.44), residues: 210 =============================================================================== Job complete usr+sys time: 868.20 seconds wall clock time: 16 minutes 3.22 seconds (963.22 seconds total)