Starting phenix.real_space_refine on Fri Sep 27 06:55:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfd_13372/09_2024/7pfd_13372.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfd_13372/09_2024/7pfd_13372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfd_13372/09_2024/7pfd_13372.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfd_13372/09_2024/7pfd_13372.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfd_13372/09_2024/7pfd_13372.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfd_13372/09_2024/7pfd_13372.cif" } resolution = 4.4 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 344 5.49 5 S 10 5.16 5 C 7520 2.51 5 N 2563 2.21 5 O 3238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13675 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "J" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 3541 Classifications: {'DNA': 172} Link IDs: {'rna3p': 171} Chain: "I" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 3511 Classifications: {'DNA': 172} Link IDs: {'rna3p': 171} Chain: "U" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 8.04, per 1000 atoms: 0.59 Number of scatterers: 13675 At special positions: 0 Unit cell: (111.3, 160.65, 114.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 344 15.00 O 3238 8.00 N 2563 7.00 C 7520 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 - 3.00 Amino acid : True - 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: 3.06 Conformation dependent library (CDL) restraints added in 996.2 milliseconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 68.8% alpha, 2.8% beta 169 base pairs and 294 stacking pairs defined. Time for finding SS restraints: 7.34 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.842A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.537A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.533A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.507A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.564A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.796A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.544A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.641A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.313A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.573A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 Processing helix chain 'U' and resid 38 through 49 removed outlier: 3.967A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 69 Processing helix chain 'U' and resid 75 through 90 removed outlier: 3.971A pdb=" N LYS U 84 " --> pdb=" O LYS U 80 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL U 87 " --> pdb=" O LEU U 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.283A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.192A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.846A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.967A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.503A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'U' and resid 92 through 94 429 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 431 hydrogen bonds 862 hydrogen bond angles 0 basepair planarities 169 basepair parallelities 294 stacking parallelities Total time for adding SS restraints: 6.66 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2420 1.33 - 1.45: 5050 1.45 - 1.57: 6440 1.57 - 1.69: 686 1.69 - 1.82: 20 Bond restraints: 14616 Sorted by residual: bond pdb=" C3' DG J 763 " pdb=" O3' DG J 763 " ideal model delta sigma weight residual 1.422 1.497 -0.075 3.00e-02 1.11e+03 6.24e+00 bond pdb=" CG GLU H 113 " pdb=" CD GLU H 113 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.76e+00 bond pdb=" C3' DG I 119 " pdb=" O3' DG I 119 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.47e+00 bond pdb=" C3' DT I 133 " pdb=" O3' DT I 133 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 3.04e+00 bond pdb=" CG GLU F 63 " pdb=" CD GLU F 63 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.68e+00 ... (remaining 14611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 20936 2.99 - 5.98: 237 5.98 - 8.97: 30 8.97 - 11.96: 2 11.96 - 14.95: 3 Bond angle restraints: 21208 Sorted by residual: angle pdb=" N GLU H 113 " pdb=" CA GLU H 113 " pdb=" CB GLU H 113 " ideal model delta sigma weight residual 110.28 119.29 -9.01 1.55e+00 4.16e-01 3.38e+01 angle pdb=" N GLU F 63 " pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " ideal model delta sigma weight residual 110.16 118.40 -8.24 1.48e+00 4.57e-01 3.10e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 110.77 121.25 -10.48 1.93e+00 2.68e-01 2.95e+01 angle pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 angle pdb=" CA LEU F 62 " pdb=" CB LEU F 62 " pdb=" CG LEU F 62 " ideal model delta sigma weight residual 116.30 131.25 -14.95 3.50e+00 8.16e-02 1.82e+01 ... (remaining 21203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 6098 35.86 - 71.73: 1769 71.73 - 107.59: 49 107.59 - 143.46: 1 143.46 - 179.32: 2 Dihedral angle restraints: 7919 sinusoidal: 5488 harmonic: 2431 Sorted by residual: dihedral pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta harmonic sigma weight residual 180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" C4' DG I 119 " pdb=" C3' DG I 119 " pdb=" O3' DG I 119 " pdb=" P DC I 120 " ideal model delta sinusoidal sigma weight residual 220.00 40.68 179.32 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA PHE A 84 " pdb=" C PHE A 84 " pdb=" N GLN A 85 " pdb=" CA GLN A 85 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 7916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1705 0.047 - 0.094: 575 0.094 - 0.142: 107 0.142 - 0.189: 21 0.189 - 0.236: 8 Chirality restraints: 2416 Sorted by residual: chirality pdb=" CB THR G 59 " pdb=" CA THR G 59 " pdb=" OG1 THR G 59 " pdb=" CG2 THR G 59 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA PHE E 104 " pdb=" N PHE E 104 " pdb=" C PHE E 104 " pdb=" CB PHE E 104 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2413 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.052 5.00e-02 4.00e+02 7.88e-02 9.94e+00 pdb=" N PRO G 80 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 113 " 0.015 2.00e-02 2.50e+03 3.14e-02 9.87e+00 pdb=" CD GLU H 113 " -0.054 2.00e-02 2.50e+03 pdb=" OE1 GLU H 113 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU H 113 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 70 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.49e+00 pdb=" C VAL F 70 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL F 70 " -0.019 2.00e-02 2.50e+03 pdb=" N THR F 71 " -0.017 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2628 2.78 - 3.31: 12748 3.31 - 3.84: 30087 3.84 - 4.37: 33559 4.37 - 4.90: 45685 Nonbonded interactions: 124707 Sorted by model distance: nonbonded pdb=" O VAL D 118 " pdb=" OG1 THR D 122 " model vdw 2.245 3.040 nonbonded pdb=" O LYS G 15 " pdb=" NH1 ARG G 20 " model vdw 2.279 3.120 nonbonded pdb=" NH1 ARG C 81 " pdb=" O VAL C 107 " model vdw 2.290 3.120 nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 71 " model vdw 2.293 3.040 nonbonded pdb=" NH2 ARG D 33 " pdb=" O2 DC I 51 " model vdw 2.296 3.120 ... (remaining 124702 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 38.180 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 : 0.006 0.075 14616 Z= 0.313 Angle : 0.915 14.946 21208 Z= 0.523 Chirality : 0.049 0.236 2416 Planarity : 0.007 0.079 1488 Dihedral : 29.935 179.324 6353 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 825 helix: 0.04 (0.20), residues: 560 sheet: -3.84 (0.84), residues: 10 loop : -0.91 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS D 109 PHE 0.020 0.003 PHE C 25 TYR 0.023 0.003 TYR G 50 ARG 0.008 0.001 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8488 (t80) cc_final: 0.8221 (t80) REVERT: A 104 PHE cc_start: 0.9578 (m-10) cc_final: 0.9329 (m-80) REVERT: E 105 GLU cc_start: 0.9361 (mt-10) cc_final: 0.8967 (mm-30) REVERT: G 34 LEU cc_start: 0.8427 (mt) cc_final: 0.8216 (mt) REVERT: H 98 VAL cc_start: 0.9711 (t) cc_final: 0.9466 (p) REVERT: H 102 LEU cc_start: 0.8816 (mp) cc_final: 0.8413 (tp) REVERT: H 105 GLU cc_start: 0.9730 (tp30) cc_final: 0.9527 (tm-30) REVERT: H 106 LEU cc_start: 0.9767 (mt) cc_final: 0.9413 (mt) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2319 time to fit residues: 36.5234 Evaluate side-chains 70 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.131 14616 Z= 0.420 Angle : 0.795 11.679 21208 Z= 0.463 Chirality : 0.043 0.167 2416 Planarity : 0.007 0.076 1488 Dihedral : 33.908 178.886 4701 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 26.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.14 % Allowed : 5.34 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.27), residues: 825 helix: 0.49 (0.20), residues: 584 sheet: -3.89 (1.03), residues: 10 loop : -1.02 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS F 75 PHE 0.020 0.003 PHE D 70 TYR 0.025 0.003 TYR G 57 ARG 0.009 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 ASP cc_start: 0.8707 (m-30) cc_final: 0.8476 (m-30) REVERT: E 104 PHE cc_start: 0.9527 (m-80) cc_final: 0.9268 (m-80) REVERT: H 106 LEU cc_start: 0.9667 (mt) cc_final: 0.9399 (pp) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.2296 time to fit residues: 30.0293 Evaluate side-chains 60 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN E 76 GLN E 93 GLN E 108 ASN F 93 GLN H 82 HIS H 109 HIS U 75 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14616 Z= 0.267 Angle : 0.685 8.404 21208 Z= 0.409 Chirality : 0.038 0.167 2416 Planarity : 0.005 0.065 1488 Dihedral : 33.652 178.828 4701 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.29 % Allowed : 3.46 % Favored : 96.25 % 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: 0.40 (0.28), residues: 825 helix: 0.92 (0.21), residues: 580 sheet: -3.52 (1.24), residues: 10 loop : -1.07 (0.35), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.029 0.003 PHE A 104 TYR 0.021 0.002 TYR D 42 ARG 0.011 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8432 (t80) cc_final: 0.8179 (t80) REVERT: D 42 TYR cc_start: 0.9193 (m-80) cc_final: 0.8983 (m-80) REVERT: E 104 PHE cc_start: 0.9665 (m-80) cc_final: 0.9245 (m-80) REVERT: F 53 GLU cc_start: 0.9605 (tp30) cc_final: 0.9335 (tm-30) REVERT: G 73 ASN cc_start: 0.8929 (t0) cc_final: 0.8699 (t0) REVERT: H 105 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8713 (tm-30) REVERT: H 108 LYS cc_start: 0.9742 (pttp) cc_final: 0.9541 (pttp) REVERT: H 109 HIS cc_start: 0.9623 (m-70) cc_final: 0.9271 (m170) outliers start: 2 outliers final: 0 residues processed: 95 average time/residue: 0.2438 time to fit residues: 34.8606 Evaluate side-chains 70 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 109 optimal weight: 40.0000 chunk 97 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN H 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.074 14616 Z= 0.518 Angle : 0.911 9.384 21208 Z= 0.531 Chirality : 0.051 0.237 2416 Planarity : 0.008 0.088 1488 Dihedral : 34.880 177.937 4701 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 42.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.14 % Allowed : 6.20 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.27), residues: 825 helix: -0.16 (0.20), residues: 568 sheet: -3.15 (1.40), residues: 10 loop : -1.34 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.003 HIS H 109 PHE 0.019 0.004 PHE B 100 TYR 0.028 0.004 TYR C 39 ARG 0.008 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 PHE cc_start: 0.9738 (m-80) cc_final: 0.9397 (m-80) REVERT: F 53 GLU cc_start: 0.9529 (tp30) cc_final: 0.9227 (tm-30) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.2469 time to fit residues: 29.4601 Evaluate side-chains 57 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 0.0870 chunk 93 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS E 39 HIS E 76 GLN E 108 ASN G 38 ASN H 82 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14616 Z= 0.290 Angle : 0.732 8.693 21208 Z= 0.433 Chirality : 0.041 0.172 2416 Planarity : 0.005 0.061 1488 Dihedral : 34.527 179.871 4701 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.29 % Allowed : 3.32 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.27), residues: 825 helix: 0.41 (0.21), residues: 572 sheet: -2.51 (1.73), residues: 10 loop : -1.47 (0.34), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 109 PHE 0.029 0.002 PHE A 104 TYR 0.015 0.002 TYR D 42 ARG 0.006 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8510 (t80) cc_final: 0.8288 (t80) REVERT: B 66 ILE cc_start: 0.9797 (tp) cc_final: 0.9588 (pt) REVERT: D 42 TYR cc_start: 0.9421 (m-80) cc_final: 0.9113 (m-80) REVERT: E 81 ASP cc_start: 0.9408 (p0) cc_final: 0.9196 (m-30) REVERT: F 53 GLU cc_start: 0.9560 (tp30) cc_final: 0.9317 (tm-30) REVERT: G 73 ASN cc_start: 0.8947 (t0) cc_final: 0.8739 (t0) REVERT: H 108 LYS cc_start: 0.9677 (pttp) cc_final: 0.9436 (ptpp) REVERT: H 109 HIS cc_start: 0.9532 (m-70) cc_final: 0.9258 (m-70) outliers start: 2 outliers final: 0 residues processed: 91 average time/residue: 0.2394 time to fit residues: 32.8379 Evaluate side-chains 68 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 57 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN E 76 GLN E 108 ASN ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14616 Z= 0.388 Angle : 0.781 8.612 21208 Z= 0.457 Chirality : 0.044 0.193 2416 Planarity : 0.006 0.063 1488 Dihedral : 34.798 179.283 4701 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 30.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 825 helix: 0.13 (0.21), residues: 566 sheet: -2.50 (1.80), residues: 10 loop : -1.60 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS H 109 PHE 0.016 0.003 PHE B 100 TYR 0.031 0.003 TYR H 42 ARG 0.022 0.001 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8516 (t80) cc_final: 0.8293 (t80) REVERT: B 66 ILE cc_start: 0.9799 (tp) cc_final: 0.9593 (pt) REVERT: C 38 ASN cc_start: 0.7207 (t0) cc_final: 0.6921 (t0) REVERT: D 71 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8882 (mm-30) REVERT: F 53 GLU cc_start: 0.9511 (tp30) cc_final: 0.9236 (tm-30) REVERT: G 38 ASN cc_start: 0.8630 (m110) cc_final: 0.8183 (m-40) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2493 time to fit residues: 30.5341 Evaluate side-chains 63 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS E 76 GLN E 93 GLN E 108 ASN F 64 ASN H 109 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.7100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14616 Z= 0.289 Angle : 0.727 8.679 21208 Z= 0.428 Chirality : 0.041 0.164 2416 Planarity : 0.005 0.061 1488 Dihedral : 34.675 177.732 4701 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.28), residues: 825 helix: 0.44 (0.21), residues: 568 sheet: -2.46 (1.94), residues: 10 loop : -1.52 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS H 109 PHE 0.046 0.002 PHE A 104 TYR 0.015 0.002 TYR C 39 ARG 0.005 0.001 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8530 (t80) cc_final: 0.8301 (t80) REVERT: B 66 ILE cc_start: 0.9825 (tp) cc_final: 0.9612 (pt) REVERT: D 42 TYR cc_start: 0.9461 (m-80) cc_final: 0.9144 (m-80) REVERT: D 71 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8927 (mm-30) REVERT: F 53 GLU cc_start: 0.9551 (tp30) cc_final: 0.9317 (tm-30) REVERT: G 73 ASN cc_start: 0.9015 (t0) cc_final: 0.8803 (t0) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2487 time to fit residues: 32.7681 Evaluate side-chains 70 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.7694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14616 Z= 0.318 Angle : 0.739 8.530 21208 Z= 0.434 Chirality : 0.041 0.169 2416 Planarity : 0.006 0.060 1488 Dihedral : 34.706 176.612 4701 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.28), residues: 825 helix: 0.42 (0.21), residues: 570 sheet: -2.44 (1.99), residues: 10 loop : -1.58 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS H 109 PHE 0.017 0.002 PHE A 104 TYR 0.044 0.002 TYR H 42 ARG 0.007 0.001 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9372 (tt0) cc_final: 0.8708 (tp40) REVERT: A 104 PHE cc_start: 0.9664 (m-80) cc_final: 0.9406 (m-80) REVERT: B 66 ILE cc_start: 0.9821 (tp) cc_final: 0.9598 (pt) REVERT: D 71 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8915 (mm-30) REVERT: E 104 PHE cc_start: 0.9700 (m-80) cc_final: 0.9330 (m-80) REVERT: E 120 MET cc_start: 0.5099 (mtt) cc_final: 0.4888 (mtt) REVERT: G 73 ASN cc_start: 0.9046 (t0) cc_final: 0.8833 (t0) REVERT: H 73 ILE cc_start: 0.9070 (mp) cc_final: 0.8814 (tp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2609 time to fit residues: 33.2072 Evaluate side-chains 67 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.8481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 14616 Z= 0.370 Angle : 0.777 8.307 21208 Z= 0.455 Chirality : 0.043 0.202 2416 Planarity : 0.006 0.061 1488 Dihedral : 34.949 176.112 4701 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 29.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.74 (0.27), residues: 825 helix: 0.13 (0.20), residues: 570 sheet: -2.64 (1.90), residues: 10 loop : -1.72 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 75 PHE 0.014 0.002 PHE B 100 TYR 0.019 0.002 TYR H 40 ARG 0.006 0.001 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9386 (tt0) cc_final: 0.8625 (tp-100) REVERT: A 104 PHE cc_start: 0.9648 (m-80) cc_final: 0.9433 (m-80) REVERT: B 66 ILE cc_start: 0.9836 (tp) cc_final: 0.9632 (pt) REVERT: D 42 TYR cc_start: 0.9444 (m-80) cc_final: 0.9093 (m-80) REVERT: D 71 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8814 (mm-30) REVERT: E 104 PHE cc_start: 0.9703 (m-80) cc_final: 0.9349 (m-80) REVERT: G 73 ASN cc_start: 0.9118 (t0) cc_final: 0.8902 (t0) REVERT: H 42 TYR cc_start: 0.9614 (m-80) cc_final: 0.9410 (m-80) REVERT: H 99 ARG cc_start: 0.9174 (mtt90) cc_final: 0.8903 (mtt90) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2493 time to fit residues: 29.0044 Evaluate side-chains 62 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.9491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 14616 Z= 0.406 Angle : 0.823 14.679 21208 Z= 0.478 Chirality : 0.045 0.202 2416 Planarity : 0.006 0.060 1488 Dihedral : 35.226 173.683 4701 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 33.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.99 (0.27), residues: 825 helix: -0.12 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.67 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS F 75 PHE 0.025 0.003 PHE E 84 TYR 0.018 0.002 TYR D 40 ARG 0.014 0.001 ARG E 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9388 (tt0) cc_final: 0.8623 (tp-100) REVERT: G 73 ASN cc_start: 0.9216 (t0) cc_final: 0.9001 (t0) REVERT: H 99 ARG cc_start: 0.9145 (mtt90) cc_final: 0.8903 (ptp90) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2508 time to fit residues: 28.9811 Evaluate side-chains 61 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.028766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.023192 restraints weight = 221903.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.024071 restraints weight = 120550.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.024685 restraints weight = 79915.579| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.9614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14616 Z= 0.313 Angle : 0.758 8.711 21208 Z= 0.443 Chirality : 0.042 0.195 2416 Planarity : 0.005 0.059 1488 Dihedral : 35.024 172.569 4701 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.28), residues: 825 helix: 0.24 (0.21), residues: 570 sheet: -2.91 (1.75), residues: 10 loop : -1.71 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.013 0.002 PHE B 100 TYR 0.019 0.002 TYR D 40 ARG 0.005 0.001 ARG A 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1862.55 seconds wall clock time: 34 minutes 54.18 seconds (2094.18 seconds total)