Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 14:38:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktq_23026/04_2023/7ktq_23026.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktq_23026/04_2023/7ktq_23026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktq_23026/04_2023/7ktq_23026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktq_23026/04_2023/7ktq_23026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktq_23026/04_2023/7ktq_23026.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktq_23026/04_2023/7ktq_23026.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 331 5.49 5 S 12 5.16 5 C 6973 2.51 5 N 2384 2.21 5 O 3045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H ASP 65": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12745 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3343 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "J" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3441 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Time building chain proxies: 6.79, per 1000 atoms: 0.53 Number of scatterers: 12745 At special positions: 0 Unit cell: (76.95, 121.5, 147.15, 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 12 16.00 P 331 15.00 O 3045 8.00 N 2384 7.00 C 6973 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: 6.61 Conformation dependent library (CDL) restraints added in 969.6 milliseconds 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1408 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 71.0% alpha, 3.2% beta 117 base pairs and 288 stacking pairs defined. Time for finding SS restraints: 5.13 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.709A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.551A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.559A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 3.652A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.710A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.651A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.552A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.559A 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 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 3.674A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.715A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.904A 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 98 removed outlier: 6.310A 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: 7.173A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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: 6.964A 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: 7.192A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 400 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 300 hydrogen bonds 596 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 288 stacking parallelities Total time for adding SS restraints: 4.15 Time building geometry restraints manager: 6.99 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: 2203 1.33 - 1.45: 4715 1.45 - 1.57: 6049 1.57 - 1.69: 661 1.69 - 1.80: 22 Bond restraints: 13650 Sorted by residual: bond pdb=" O5' DA J 83 " pdb=" C5' DA J 83 " ideal model delta sigma weight residual 1.423 1.351 0.072 3.00e-02 1.11e+03 5.72e+00 bond pdb=" C3' DT J 106 " pdb=" O3' DT J 106 " ideal model delta sigma weight residual 1.422 1.487 -0.065 3.00e-02 1.11e+03 4.62e+00 bond pdb=" O5' DC I 64 " pdb=" C5' DC I 64 " ideal model delta sigma weight residual 1.423 1.360 0.063 3.00e-02 1.11e+03 4.41e+00 bond pdb=" O5' DG J 102 " pdb=" C5' DG J 102 " ideal model delta sigma weight residual 1.423 1.363 0.060 3.00e-02 1.11e+03 3.99e+00 bond pdb=" O5' DT J 17 " pdb=" C5' DT J 17 " ideal model delta sigma weight residual 1.423 1.366 0.057 3.00e-02 1.11e+03 3.56e+00 ... (remaining 13645 not shown) Histogram of bond angle deviations from ideal: 98.17 - 105.06: 1386 105.06 - 111.96: 7302 111.96 - 118.85: 3852 118.85 - 125.74: 6253 125.74 - 132.63: 1072 Bond angle restraints: 19865 Sorted by residual: angle pdb=" C ARG E 40 " pdb=" N TYR E 41 " pdb=" CA TYR E 41 " ideal model delta sigma weight residual 122.03 113.80 8.23 2.01e+00 2.48e-01 1.68e+01 angle pdb=" N ILE F 26 " pdb=" CA ILE F 26 " pdb=" C ILE F 26 " ideal model delta sigma weight residual 112.50 107.10 5.40 1.39e+00 5.18e-01 1.51e+01 angle pdb=" C4' DC J 82 " pdb=" C3' DC J 82 " pdb=" O3' DC J 82 " ideal model delta sigma weight residual 110.00 104.27 5.73 1.50e+00 4.44e-01 1.46e+01 angle pdb=" C3' DT J 106 " pdb=" O3' DT J 106 " pdb=" P DG J 107 " ideal model delta sigma weight residual 120.20 125.30 -5.10 1.50e+00 4.44e-01 1.16e+01 angle pdb=" N ILE B 26 " pdb=" CA ILE B 26 " pdb=" C ILE B 26 " ideal model delta sigma weight residual 112.50 107.99 4.51 1.39e+00 5.18e-01 1.05e+01 ... (remaining 19860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 5440 35.95 - 71.89: 1588 71.89 - 107.84: 21 107.84 - 143.79: 0 143.79 - 179.74: 5 Dihedral angle restraints: 7054 sinusoidal: 4872 harmonic: 2182 Sorted by residual: dihedral pdb=" C4' DC I 3 " pdb=" C3' DC I 3 " pdb=" O3' DC I 3 " pdb=" P DC I 4 " ideal model delta sinusoidal sigma weight residual -140.00 39.74 -179.74 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 104 " pdb=" C3' DG I 104 " pdb=" O3' DG I 104 " pdb=" P DC I 105 " ideal model delta sinusoidal sigma weight residual 220.00 40.45 179.55 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 106 " pdb=" C3' DT J 106 " pdb=" O3' DT J 106 " pdb=" P DG J 107 " ideal model delta sinusoidal sigma weight residual 220.00 42.30 177.70 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1790 0.059 - 0.118: 418 0.118 - 0.177: 51 0.177 - 0.236: 1 0.236 - 0.295: 2 Chirality restraints: 2262 Sorted by residual: chirality pdb=" CG LEU G 115 " pdb=" CB LEU G 115 " pdb=" CD1 LEU G 115 " pdb=" CD2 LEU G 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C1' DG J 66 " pdb=" O4' DG J 66 " pdb=" C2' DG J 66 " pdb=" N9 DG J 66 " both_signs ideal model delta sigma weight residual False 2.42 2.18 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C4' DA J 83 " pdb=" C5' DA J 83 " pdb=" O4' DA J 83 " pdb=" C3' DA J 83 " both_signs ideal model delta sigma weight residual False -2.53 -2.31 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2259 not shown) Planarity restraints: 1368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 106 " 0.005 2.00e-02 2.50e+03 3.37e-02 2.55e+01 pdb=" N1 DC I 106 " -0.025 2.00e-02 2.50e+03 pdb=" C2 DC I 106 " 0.083 2.00e-02 2.50e+03 pdb=" O2 DC I 106 " -0.045 2.00e-02 2.50e+03 pdb=" N3 DC I 106 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DC I 106 " 0.016 2.00e-02 2.50e+03 pdb=" N4 DC I 106 " -0.014 2.00e-02 2.50e+03 pdb=" C5 DC I 106 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC I 106 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 87 " -0.043 2.00e-02 2.50e+03 2.87e-02 1.86e+01 pdb=" N1 DC J 87 " 0.068 2.00e-02 2.50e+03 pdb=" C2 DC J 87 " -0.027 2.00e-02 2.50e+03 pdb=" O2 DC J 87 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DC J 87 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC J 87 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC J 87 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC J 87 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DC J 87 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 106 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C HIS H 106 " 0.073 2.00e-02 2.50e+03 pdb=" O HIS H 106 " -0.027 2.00e-02 2.50e+03 pdb=" N ALA H 107 " -0.025 2.00e-02 2.50e+03 ... (remaining 1365 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1483 2.74 - 3.28: 10850 3.28 - 3.82: 24023 3.82 - 4.36: 29764 4.36 - 4.90: 41980 Nonbonded interactions: 108100 Sorted by model distance: nonbonded pdb=" OE1 GLU B 74 " pdb=" NH2 ARG D 96 " model vdw 2.201 2.520 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.248 2.440 nonbonded pdb=" C2' DA J 20 " pdb=" C7 DT J 21 " model vdw 2.274 3.860 nonbonded pdb=" OE1 GLU F 74 " pdb=" NH2 ARG H 96 " model vdw 2.295 2.520 nonbonded pdb=" O6 DG I 44 " pdb=" N4 DC J 124 " model vdw 2.313 2.520 ... (remaining 108095 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' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 117) 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 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: 1.420 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: 7.050 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 39.050 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 51.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 : 0.008 0.072 13650 Z= 0.456 Angle : 0.840 8.228 19865 Z= 0.523 Chirality : 0.050 0.295 2262 Planarity : 0.009 0.043 1368 Dihedral : 29.359 179.736 5646 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.24), residues: 736 helix: -1.35 (0.18), residues: 532 sheet: None (None), residues: 0 loop : -1.86 (0.34), residues: 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 0.991 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.4301 time to fit residues: 101.0287 Evaluate side-chains 127 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN B 93 GLN D 81 ASN F 27 GLN G 38 ASN G 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 13650 Z= 0.212 Angle : 0.554 5.425 19865 Z= 0.334 Chirality : 0.033 0.162 2262 Planarity : 0.005 0.043 1368 Dihedral : 32.940 178.766 4164 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.29), residues: 736 helix: 1.50 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -1.24 (0.37), residues: 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 1.001 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 138 average time/residue: 0.3141 time to fit residues: 58.5140 Evaluate side-chains 129 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1113 time to fit residues: 2.5741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 93 GLN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 13650 Z= 0.336 Angle : 0.601 5.852 19865 Z= 0.356 Chirality : 0.036 0.146 2262 Planarity : 0.005 0.039 1368 Dihedral : 32.725 178.508 4164 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 1.12 % 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: 1.90 (0.30), residues: 736 helix: 2.07 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.17 (0.39), residues: 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 1.035 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 128 average time/residue: 0.3615 time to fit residues: 60.7096 Evaluate side-chains 118 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 0.858 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1912 time to fit residues: 2.2686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN F 93 GLN G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 13650 Z= 0.201 Angle : 0.549 5.479 19865 Z= 0.332 Chirality : 0.033 0.137 2262 Planarity : 0.004 0.040 1368 Dihedral : 32.680 178.398 4164 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.30), residues: 736 helix: 2.50 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -1.13 (0.39), residues: 194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 0.960 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 123 average time/residue: 0.3383 time to fit residues: 55.5447 Evaluate side-chains 123 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1108 time to fit residues: 1.9847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 68 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 33 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 13650 Z= 0.182 Angle : 0.528 5.348 19865 Z= 0.321 Chirality : 0.032 0.143 2262 Planarity : 0.004 0.038 1368 Dihedral : 32.536 178.336 4164 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.31), residues: 736 helix: 2.75 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -1.03 (0.39), residues: 194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 1.001 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 123 average time/residue: 0.3318 time to fit residues: 54.7624 Evaluate side-chains 116 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2687 time to fit residues: 1.9161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN D 46 HIS D 92 GLN G 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 13650 Z= 0.214 Angle : 0.524 5.355 19865 Z= 0.317 Chirality : 0.032 0.137 2262 Planarity : 0.004 0.037 1368 Dihedral : 32.373 178.427 4164 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.31), residues: 736 helix: 2.93 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.93 (0.40), residues: 194 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 0.971 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 121 average time/residue: 0.3325 time to fit residues: 53.6126 Evaluate side-chains 122 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1021 time to fit residues: 2.0080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 0.0040 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 13650 Z= 0.174 Angle : 0.520 5.373 19865 Z= 0.316 Chirality : 0.031 0.133 2262 Planarity : 0.004 0.035 1368 Dihedral : 32.363 178.398 4164 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.31), residues: 736 helix: 3.01 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.88 (0.41), residues: 194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.926 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.3531 time to fit residues: 58.9843 Evaluate side-chains 120 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN H 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 13650 Z= 0.269 Angle : 0.551 5.395 19865 Z= 0.330 Chirality : 0.034 0.140 2262 Planarity : 0.004 0.034 1368 Dihedral : 32.399 178.851 4164 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.31), residues: 736 helix: 2.82 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.99 (0.41), residues: 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 0.842 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 120 average time/residue: 0.3442 time to fit residues: 54.4173 Evaluate side-chains 121 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1161 time to fit residues: 1.4163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 13650 Z= 0.206 Angle : 0.538 7.087 19865 Z= 0.325 Chirality : 0.032 0.135 2262 Planarity : 0.004 0.034 1368 Dihedral : 32.384 178.795 4164 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.31), residues: 736 helix: 2.88 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.96 (0.41), residues: 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.954 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 118 average time/residue: 0.3205 time to fit residues: 50.3329 Evaluate side-chains 120 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1233 time to fit residues: 1.4651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 13650 Z= 0.192 Angle : 0.529 5.589 19865 Z= 0.320 Chirality : 0.032 0.135 2262 Planarity : 0.004 0.035 1368 Dihedral : 32.358 178.768 4164 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.31), residues: 736 helix: 2.93 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.93 (0.41), residues: 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.880 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.3398 time to fit residues: 54.0192 Evaluate side-chains 119 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.152596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.103112 restraints weight = 17714.541| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.01 r_work: 0.2969 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 13650 Z= 0.211 Angle : 0.527 5.411 19865 Z= 0.319 Chirality : 0.032 0.136 2262 Planarity : 0.004 0.035 1368 Dihedral : 32.328 178.760 4164 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.31), residues: 736 helix: 2.94 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.92 (0.41), residues: 192 =============================================================================== Job complete usr+sys time: 2253.55 seconds wall clock time: 41 minutes 31.07 seconds (2491.07 seconds total)