Starting phenix.real_space_refine (version: 1.21rc1) on Thu Sep 28 00:32:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl4_24514/09_2023/7rl4_24514.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl4_24514/09_2023/7rl4_24514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl4_24514/09_2023/7rl4_24514.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl4_24514/09_2023/7rl4_24514.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl4_24514/09_2023/7rl4_24514.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rl4_24514/09_2023/7rl4_24514.pdb" } resolution = 2.86 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= 0.002 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 80 5.16 5 C 2920 2.51 5 N 860 2.21 5 O 760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 4620 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "K" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "P" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "C" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "G" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "L" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "Q" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "D" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "H" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "M" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "R" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "E" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "I" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "N" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "S" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "F" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "J" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "O" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "T" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 231 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Time building chain proxies: 2.74, per 1000 atoms: 0.59 Number of scatterers: 4620 At special positions: 0 Unit cell: (91.908, 85.284, 47.196, 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 80 16.00 O 760 8.00 N 860 7.00 C 2920 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=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 688.7 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1080 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 109 through 112 removed outlier: 6.433A pdb=" N LYS C 110 " --> pdb=" O HIS D 111 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS A 110 " --> pdb=" O HIS E 111 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS E 110 " --> pdb=" O HIS F 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.446A pdb=" N MET A 134 " --> pdb=" O SER D 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 138 through 140 removed outlier: 6.458A pdb=" N ILE C 139 " --> pdb=" O HIS D 140 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 139 " --> pdb=" O HIS E 140 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE E 139 " --> pdb=" O HIS F 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 109 through 112 removed outlier: 6.412A pdb=" N LYS G 110 " --> pdb=" O HIS H 111 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS B 110 " --> pdb=" O HIS I 111 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS I 110 " --> pdb=" O HIS J 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 133 through 135 removed outlier: 6.381A pdb=" N MET B 134 " --> pdb=" O SER H 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 138 through 140 removed outlier: 6.339A pdb=" N ILE G 139 " --> pdb=" O HIS H 140 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE B 139 " --> pdb=" O HIS I 140 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE I 139 " --> pdb=" O HIS J 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 109 through 112 removed outlier: 6.474A pdb=" N LYS L 110 " --> pdb=" O HIS M 111 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS K 110 " --> pdb=" O HIS N 111 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS N 110 " --> pdb=" O HIS O 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 133 through 135 removed outlier: 6.399A pdb=" N MET K 134 " --> pdb=" O SER M 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 138 through 140 removed outlier: 6.491A pdb=" N ILE L 139 " --> pdb=" O HIS M 140 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE K 139 " --> pdb=" O HIS N 140 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE N 139 " --> pdb=" O HIS O 140 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 109 through 112 removed outlier: 6.364A pdb=" N LYS Q 110 " --> pdb=" O HIS R 111 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS P 110 " --> pdb=" O HIS S 111 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS S 110 " --> pdb=" O HIS T 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 133 through 135 removed outlier: 6.425A pdb=" N MET P 134 " --> pdb=" O SER R 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 138 through 140 removed outlier: 6.298A pdb=" N ILE Q 139 " --> pdb=" O HIS R 140 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE P 139 " --> pdb=" O HIS S 140 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE S 139 " --> pdb=" O HIS T 140 " (cutoff:3.500A) 44 hydrogen bonds defined for protein. 132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1510 1.33 - 1.45: 694 1.45 - 1.56: 2336 1.56 - 1.68: 0 1.68 - 1.79: 160 Bond restraints: 4700 Sorted by residual: bond pdb=" CB VAL T 122 " pdb=" CG1 VAL T 122 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.46e+00 bond pdb=" CB VAL L 122 " pdb=" CG1 VAL L 122 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.40e+00 bond pdb=" CB VAL I 122 " pdb=" CG1 VAL I 122 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.39e+00 bond pdb=" CB VAL F 122 " pdb=" CG1 VAL F 122 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.38e+00 bond pdb=" CB VAL P 122 " pdb=" CG1 VAL P 122 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.36e+00 ... (remaining 4695 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.22: 140 105.22 - 111.76: 2171 111.76 - 118.30: 1389 118.30 - 124.84: 2500 124.84 - 131.38: 60 Bond angle restraints: 6260 Sorted by residual: angle pdb=" C ALA N 133 " pdb=" N MET N 134 " pdb=" CA MET N 134 " ideal model delta sigma weight residual 123.05 118.97 4.08 1.40e+00 5.10e-01 8.48e+00 angle pdb=" C ALA O 133 " pdb=" N MET O 134 " pdb=" CA MET O 134 " ideal model delta sigma weight residual 123.05 118.97 4.08 1.40e+00 5.10e-01 8.48e+00 angle pdb=" C ALA M 133 " pdb=" N MET M 134 " pdb=" CA MET M 134 " ideal model delta sigma weight residual 123.05 118.98 4.07 1.40e+00 5.10e-01 8.47e+00 angle pdb=" C ALA K 133 " pdb=" N MET K 134 " pdb=" CA MET K 134 " ideal model delta sigma weight residual 123.05 118.99 4.06 1.40e+00 5.10e-01 8.43e+00 angle pdb=" C ALA Q 133 " pdb=" N MET Q 134 " pdb=" CA MET Q 134 " ideal model delta sigma weight residual 123.05 118.99 4.06 1.40e+00 5.10e-01 8.39e+00 ... (remaining 6255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.17: 2132 11.17 - 22.33: 288 22.33 - 33.49: 160 33.49 - 44.66: 80 44.66 - 55.82: 20 Dihedral angle restraints: 2680 sinusoidal: 920 harmonic: 1760 Sorted by residual: dihedral pdb=" CA GLY N 131 " pdb=" C GLY N 131 " pdb=" N SER N 132 " pdb=" CA SER N 132 " ideal model delta harmonic sigma weight residual -180.00 -163.23 -16.77 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA GLY K 131 " pdb=" C GLY K 131 " pdb=" N SER K 132 " pdb=" CA SER K 132 " ideal model delta harmonic sigma weight residual -180.00 -163.25 -16.75 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA GLY M 131 " pdb=" C GLY M 131 " pdb=" N SER M 132 " pdb=" CA SER M 132 " ideal model delta harmonic sigma weight residual -180.00 -163.25 -16.75 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 2677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 338 0.046 - 0.092: 262 0.092 - 0.137: 13 0.137 - 0.183: 27 0.183 - 0.229: 20 Chirality restraints: 660 Sorted by residual: chirality pdb=" CB VAL S 122 " pdb=" CA VAL S 122 " pdb=" CG1 VAL S 122 " pdb=" CG2 VAL S 122 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL T 122 " pdb=" CA VAL T 122 " pdb=" CG1 VAL T 122 " pdb=" CG2 VAL T 122 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL R 122 " pdb=" CA VAL R 122 " pdb=" CG1 VAL R 122 " pdb=" CG2 VAL R 122 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 657 not shown) Planarity restraints: 800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 122 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" C VAL E 122 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL E 122 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY E 123 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 122 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.59e+00 pdb=" C VAL F 122 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL F 122 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY F 123 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 122 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C VAL A 122 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A 122 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 123 " -0.011 2.00e-02 2.50e+03 ... (remaining 797 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 2677 3.01 - 3.48: 4029 3.48 - 3.95: 6890 3.95 - 4.43: 8976 4.43 - 4.90: 15493 Nonbonded interactions: 38065 Sorted by model distance: nonbonded pdb=" OG SER I 132 " pdb=" O LEU T 130 " model vdw 2.535 2.440 nonbonded pdb=" OG SER B 132 " pdb=" O LEU S 130 " model vdw 2.535 2.440 nonbonded pdb=" O LEU P 130 " pdb=" OG SER H 132 " model vdw 2.535 2.440 nonbonded pdb=" OG SER G 132 " pdb=" O LEU R 130 " model vdw 2.535 2.440 nonbonded pdb=" OG SER S 132 " pdb=" O LEU J 130 " model vdw 2.536 2.440 ... (remaining 38060 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 0.680 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: 3.600 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.030 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 0.015 0.077 4700 Z= 1.032 Angle : 1.156 5.297 6260 Z= 0.657 Chirality : 0.071 0.229 660 Planarity : 0.006 0.019 800 Dihedral : 16.037 55.821 1600 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % 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: -4.62 (0.23), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.17), residues: 640 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 183 average time/residue: 1.0599 time to fit residues: 201.1763 Evaluate side-chains 165 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1711 time to fit residues: 0.7995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS K 140 HIS D 140 HIS E 140 HIS N 140 HIS F 140 HIS O 140 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4700 Z= 0.218 Angle : 0.578 5.953 6260 Z= 0.290 Chirality : 0.046 0.126 660 Planarity : 0.003 0.023 800 Dihedral : 4.120 12.996 700 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 9.75 % Allowed : 21.25 % Favored : 69.00 % 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: -4.54 (0.22), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.16), residues: 640 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 183 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 9 residues processed: 183 average time/residue: 1.0077 time to fit residues: 191.7853 Evaluate side-chains 184 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 175 time to evaluate : 0.637 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.9131 time to fit residues: 9.4380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 0.0020 chunk 48 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 overall best weight: 0.6970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 140 HIS ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 HIS ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 140 HIS O 140 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4700 Z= 0.201 Angle : 0.543 5.831 6260 Z= 0.267 Chirality : 0.044 0.146 660 Planarity : 0.003 0.033 800 Dihedral : 3.765 13.761 700 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 8.25 % Allowed : 27.50 % Favored : 64.25 % 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: -4.50 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.16), residues: 640 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 9 residues processed: 179 average time/residue: 0.9901 time to fit residues: 184.3920 Evaluate side-chains 180 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 171 time to evaluate : 0.495 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 0.6608 time to fit residues: 4.1044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS ** N 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.114 4700 Z= 0.705 Angle : 0.767 6.777 6260 Z= 0.386 Chirality : 0.048 0.138 660 Planarity : 0.005 0.029 800 Dihedral : 5.107 17.372 700 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 10.25 % Allowed : 29.25 % Favored : 60.50 % 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: -4.59 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.16), residues: 640 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 186 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 10 residues processed: 199 average time/residue: 0.9982 time to fit residues: 206.6244 Evaluate side-chains 189 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 179 time to evaluate : 0.483 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 2 residues processed: 8 average time/residue: 0.3453 time to fit residues: 3.6566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 ASN ** N 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 108 ASN S 111 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4700 Z= 0.240 Angle : 0.584 6.349 6260 Z= 0.288 Chirality : 0.044 0.132 660 Planarity : 0.003 0.016 800 Dihedral : 3.937 15.499 700 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 8.50 % Allowed : 33.25 % Favored : 58.25 % 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: -4.59 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.16), residues: 640 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 5 residues processed: 187 average time/residue: 1.0189 time to fit residues: 198.1095 Evaluate side-chains 183 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 0.471 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3028 time to fit residues: 2.2925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS L 140 HIS ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS ** N 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 HIS ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 4700 Z= 0.534 Angle : 0.714 6.830 6260 Z= 0.351 Chirality : 0.044 0.130 660 Planarity : 0.004 0.031 800 Dihedral : 4.687 16.705 700 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 6.75 % Allowed : 35.50 % Favored : 57.75 % 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: -4.65 (0.21), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.16), residues: 640 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 190 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 199 average time/residue: 0.9543 time to fit residues: 197.8027 Evaluate side-chains 198 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 187 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 2 residues processed: 9 average time/residue: 0.3146 time to fit residues: 3.6974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS L 140 HIS ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS ** N 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 HIS ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 4700 Z= 0.512 Angle : 0.717 7.015 6260 Z= 0.352 Chirality : 0.044 0.133 660 Planarity : 0.004 0.023 800 Dihedral : 4.709 17.083 700 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 7.25 % Allowed : 34.75 % Favored : 58.00 % 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: -4.67 (0.20), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.16), residues: 640 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 188 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 200 average time/residue: 1.0043 time to fit residues: 209.0429 Evaluate side-chains 193 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 181 time to evaluate : 0.479 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 3 residues processed: 9 average time/residue: 0.1030 time to fit residues: 1.8495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS ** N 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 HIS ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 4700 Z= 0.383 Angle : 0.674 7.349 6260 Z= 0.326 Chirality : 0.043 0.128 660 Planarity : 0.003 0.026 800 Dihedral : 4.419 16.732 700 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.50 % Allowed : 36.75 % Favored : 57.75 % 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: -4.68 (0.20), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.16), residues: 640 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 187 average time/residue: 0.9686 time to fit residues: 188.7326 Evaluate side-chains 191 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 182 time to evaluate : 0.485 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 6 average time/residue: 0.4831 time to fit residues: 3.7503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 140 HIS ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS ** N 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 HIS ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 4700 Z= 0.304 Angle : 0.649 7.168 6260 Z= 0.313 Chirality : 0.043 0.127 660 Planarity : 0.004 0.038 800 Dihedral : 4.181 15.082 700 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.75 % Allowed : 37.25 % Favored : 58.00 % 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: -4.65 (0.20), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.16), residues: 640 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 191 average time/residue: 0.9982 time to fit residues: 198.3255 Evaluate side-chains 194 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 183 time to evaluate : 0.483 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 4 residues processed: 7 average time/residue: 0.5736 time to fit residues: 4.8767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 4700 Z= 0.308 Angle : 0.689 8.423 6260 Z= 0.328 Chirality : 0.044 0.132 660 Planarity : 0.004 0.053 800 Dihedral : 4.174 16.207 700 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.75 % Allowed : 40.00 % Favored : 58.25 % 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: -4.62 (0.20), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.16), residues: 640 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 183 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 188 average time/residue: 1.0160 time to fit residues: 198.6965 Evaluate side-chains 185 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.6015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 HIS ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 HIS ** N 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 HIS ** F 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.209483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.134010 restraints weight = 3666.109| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.35 r_work: 0.3907 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.109 4700 Z= 0.642 Angle : 0.833 10.113 6260 Z= 0.405 Chirality : 0.046 0.136 660 Planarity : 0.005 0.042 800 Dihedral : 5.098 16.058 700 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.75 % Allowed : 38.00 % Favored : 58.25 % 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: -4.67 (0.20), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.16), residues: 640 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3185.98 seconds wall clock time: 56 minutes 19.33 seconds (3379.33 seconds total)