Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 03:22:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/04_2023/8g8b_29845.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/04_2023/8g8b_29845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/04_2023/8g8b_29845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/04_2023/8g8b_29845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/04_2023/8g8b_29845.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/04_2023/8g8b_29845.pdb" } resolution = 4.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 336 5.49 5 S 17 5.16 5 C 7819 2.51 5 N 2611 2.21 5 O 3284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14067 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 863 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3419 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "J" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3469 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "X" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1080 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 1 Time building chain proxies: 7.79, per 1000 atoms: 0.55 Number of scatterers: 14067 At special positions: 0 Unit cell: (80.5, 119.14, 172.27, 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 17 16.00 P 336 15.00 O 3284 8.00 N 2611 7.00 C 7819 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: 7.76 Conformation dependent library (CDL) restraints added in 1.3 seconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 10 sheets defined 74.5% alpha, 2.4% beta 161 base pairs and 290 stacking pairs defined. Time for finding SS restraints: 6.61 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.053A 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 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.736A 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 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.233A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 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 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.950A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.533A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.363A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 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 100 through 121 Processing helix chain 'X' and resid 141 through 161 Processing helix chain 'X' and resid 163 through 176 Processing helix chain 'X' and resid 180 through 189 removed outlier: 3.552A pdb=" N ILE X 184 " --> pdb=" O SER X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 193 through 211 Proline residue: X 202 - end of helix Processing helix chain 'X' and resid 215 through 220 Processing helix chain 'X' and resid 239 through 249 Processing helix chain 'X' and resid 256 through 268 removed outlier: 3.681A pdb=" N HIS X 262 " --> pdb=" O GLN X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 288 removed outlier: 4.059A pdb=" N SER X 288 " --> pdb=" O LYS X 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.928A 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: 6.705A 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: 7.125A 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 101 through 102 removed outlier: 6.758A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.760A 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: 6.981A 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 78 491 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 389 hydrogen bonds 778 hydrogen bond angles 0 basepair planarities 161 basepair parallelities 290 stacking parallelities Total time for adding SS restraints: 7.01 Time building geometry restraints manager: 8.12 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: 2622 1.33 - 1.45: 4963 1.45 - 1.57: 6717 1.57 - 1.69: 670 1.69 - 1.81: 28 Bond restraints: 15000 Sorted by residual: bond pdb=" N THR E 32 " pdb=" CA THR E 32 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.60e+00 bond pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.32e-02 5.74e+03 6.27e+00 bond pdb=" N TYR E 41 " pdb=" CA TYR E 41 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 5.86e+00 bond pdb=" C1' DC J -96 " pdb=" N1 DC J -96 " ideal model delta sigma weight residual 1.490 1.552 -0.062 3.00e-02 1.11e+03 4.20e+00 bond pdb=" C1' DC I 83 " pdb=" N1 DC I 83 " ideal model delta sigma weight residual 1.490 1.549 -0.059 3.00e-02 1.11e+03 3.88e+00 ... (remaining 14995 not shown) Histogram of bond angle deviations from ideal: 97.20 - 104.57: 1273 104.57 - 111.94: 8343 111.94 - 119.31: 4624 119.31 - 126.68: 6412 126.68 - 134.05: 1042 Bond angle restraints: 21694 Sorted by residual: angle pdb=" O3' DG J -71 " pdb=" C3' DG J -71 " pdb=" C2' DG J -71 " ideal model delta sigma weight residual 111.50 103.17 8.33 1.50e+00 4.44e-01 3.08e+01 angle pdb=" O3' DG J -73 " pdb=" C3' DG J -73 " pdb=" C2' DG J -73 " ideal model delta sigma weight residual 111.50 104.37 7.13 1.50e+00 4.44e-01 2.26e+01 angle pdb=" O3' DA I 78 " pdb=" C3' DA I 78 " pdb=" C2' DA I 78 " ideal model delta sigma weight residual 111.50 104.62 6.88 1.50e+00 4.44e-01 2.10e+01 angle pdb=" CB MET X 197 " pdb=" CG MET X 197 " pdb=" SD MET X 197 " ideal model delta sigma weight residual 112.70 124.49 -11.79 3.00e+00 1.11e-01 1.55e+01 angle pdb=" C4' DC I 75 " pdb=" C3' DC I 75 " pdb=" O3' DC I 75 " ideal model delta sigma weight residual 110.00 104.22 5.78 1.50e+00 4.44e-01 1.48e+01 ... (remaining 21689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 6146 35.81 - 71.62: 1711 71.62 - 107.42: 15 107.42 - 143.23: 2 143.23 - 179.04: 1 Dihedral angle restraints: 7875 sinusoidal: 5260 harmonic: 2615 Sorted by residual: dihedral pdb=" C4' DA I 20 " pdb=" C3' DA I 20 " pdb=" O3' DA I 20 " pdb=" P DT I 21 " ideal model delta sinusoidal sigma weight residual -140.00 39.04 -179.04 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA I 82 " pdb=" C3' DA I 82 " pdb=" O3' DA I 82 " pdb=" P DC I 83 " ideal model delta sinusoidal sigma weight residual 220.00 80.83 139.17 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 7872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1952 0.041 - 0.083: 438 0.083 - 0.124: 63 0.124 - 0.165: 10 0.165 - 0.206: 5 Chirality restraints: 2468 Sorted by residual: chirality pdb=" C3' DC I 75 " pdb=" C4' DC I 75 " pdb=" O3' DC I 75 " pdb=" C2' DC I 75 " both_signs ideal model delta sigma weight residual False -2.66 -2.87 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C3' DT J -76 " pdb=" C4' DT J -76 " pdb=" O3' DT J -76 " pdb=" C2' DT J -76 " both_signs ideal model delta sigma weight residual False -2.66 -2.85 0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" C3' DG J -71 " pdb=" C4' DG J -71 " pdb=" O3' DG J -71 " pdb=" C2' DG J -71 " both_signs ideal model delta sigma weight residual False -2.66 -2.84 0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 2465 not shown) Planarity restraints: 1582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 79 " 0.023 2.00e-02 2.50e+03 1.15e-02 3.31e+00 pdb=" N1 DT I 79 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DT I 79 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DT I 79 " -0.013 2.00e-02 2.50e+03 pdb=" N3 DT I 79 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 79 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 79 " 0.018 2.00e-02 2.50e+03 pdb=" C5 DT I 79 " -0.007 2.00e-02 2.50e+03 pdb=" C7 DT I 79 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT I 79 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 56 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C GLY F 56 " -0.031 2.00e-02 2.50e+03 pdb=" O GLY F 56 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL F 57 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO G 80 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.025 5.00e-02 4.00e+02 ... (remaining 1579 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 146 2.63 - 3.20: 11304 3.20 - 3.76: 26958 3.76 - 4.33: 36243 4.33 - 4.90: 50059 Nonbonded interactions: 124710 Sorted by model distance: nonbonded pdb=" O2 DC I 85 " pdb=" N2 DG J -85 " model vdw 2.061 2.520 nonbonded pdb=" N6 DA I 72 " pdb=" N3 DT J -72 " model vdw 2.065 2.560 nonbonded pdb=" CD PRO E 30 " pdb=" OE1 GLU X 209 " model vdw 2.132 3.440 nonbonded pdb=" N1 DA I 72 " pdb=" O2 DT J -72 " model vdw 2.152 2.496 nonbonded pdb=" O GLN X 155 " pdb=" OG1 THR X 159 " model vdw 2.276 2.440 ... (remaining 124705 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' and resid 38 through 133) } ncs_group { reference = (chain 'B' and resid 22 through 101) selection = (chain 'F' and resid 22 through 101) } 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=0.00 max=1.00 mean=0.96 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.020 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 47.050 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 : 0.004 0.062 15000 Z= 0.242 Angle : 0.639 11.794 21694 Z= 0.388 Chirality : 0.036 0.206 2468 Planarity : 0.004 0.044 1582 Dihedral : 29.040 179.040 6183 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.81 % Favored : 98.07 % Rotamer Outliers : 1.98 % 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: 1.94 (0.27), residues: 882 helix: 1.93 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -0.64 (0.37), residues: 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 312 time to evaluate : 1.067 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 2 residues processed: 323 average time/residue: 0.3474 time to fit residues: 149.2307 Evaluate side-chains 166 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2663 time to fit residues: 1.9956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 15000 Z= 0.262 Angle : 0.657 12.081 21694 Z= 0.385 Chirality : 0.036 0.175 2468 Planarity : 0.006 0.141 1582 Dihedral : 31.999 177.459 4374 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer Outliers : 0.13 % 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: 1.87 (0.27), residues: 882 helix: 1.78 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -0.35 (0.39), residues: 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 1.233 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.3328 time to fit residues: 101.6620 Evaluate side-chains 154 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 30.0000 chunk 107 optimal weight: 50.0000 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN H 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 15000 Z= 0.283 Angle : 0.643 10.766 21694 Z= 0.376 Chirality : 0.035 0.132 2468 Planarity : 0.005 0.047 1582 Dihedral : 32.528 177.076 4374 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: 1.58 (0.27), residues: 882 helix: 1.50 (0.19), residues: 663 sheet: None (None), residues: 0 loop : -0.20 (0.40), residues: 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.064 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: 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: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.3160 time to fit residues: 89.5075 Evaluate side-chains 135 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 93 GLN D 64 ASN E 76 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS H 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 15000 Z= 0.194 Angle : 0.602 11.463 21694 Z= 0.357 Chirality : 0.034 0.145 2468 Planarity : 0.004 0.052 1582 Dihedral : 32.220 175.872 4374 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.13 % 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: 1.63 (0.28), residues: 882 helix: 1.52 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -0.13 (0.40), residues: 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.147 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: 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: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.3073 time to fit residues: 82.6530 Evaluate side-chains 137 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 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 27 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 15000 Z= 0.297 Angle : 0.656 14.276 21694 Z= 0.385 Chirality : 0.036 0.146 2468 Planarity : 0.005 0.047 1582 Dihedral : 32.668 176.767 4374 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 1.34 (0.27), residues: 882 helix: 1.34 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -0.33 (0.39), residues: 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.149 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.3034 time to fit residues: 73.0069 Evaluate side-chains 119 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** C 38 ASN E 76 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15000 Z= 0.184 Angle : 0.618 12.873 21694 Z= 0.363 Chirality : 0.034 0.154 2468 Planarity : 0.004 0.048 1582 Dihedral : 32.154 175.072 4374 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 1.40 (0.28), residues: 882 helix: 1.31 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -0.05 (0.41), residues: 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.108 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3293 time to fit residues: 81.0898 Evaluate side-chains 127 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.0970 chunk 12 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- 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** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.6865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 15000 Z= 0.313 Angle : 0.675 16.600 21694 Z= 0.394 Chirality : 0.037 0.166 2468 Planarity : 0.005 0.049 1582 Dihedral : 32.676 176.491 4374 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 24.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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: 1.30 (0.27), residues: 882 helix: 1.30 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -0.27 (0.40), residues: 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.172 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 outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.3115 time to fit residues: 70.3962 Evaluate side-chains 120 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 67 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.7127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 15000 Z= 0.231 Angle : 0.651 14.830 21694 Z= 0.378 Chirality : 0.036 0.176 2468 Planarity : 0.004 0.047 1582 Dihedral : 32.498 175.176 4374 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 1.39 (0.28), residues: 882 helix: 1.34 (0.20), residues: 653 sheet: None (None), residues: 0 loop : -0.12 (0.40), residues: 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.024 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 outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2987 time to fit residues: 69.2290 Evaluate side-chains 116 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 112 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS D 44 GLN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.8403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.065 15000 Z= 0.465 Angle : 0.822 15.742 21694 Z= 0.477 Chirality : 0.044 0.182 2468 Planarity : 0.006 0.056 1582 Dihedral : 33.907 175.506 4374 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 39.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.27), residues: 882 helix: 0.63 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -0.64 (0.40), residues: 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.235 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.3040 time to fit residues: 63.4052 Evaluate side-chains 105 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.8451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 15000 Z= 0.320 Angle : 0.719 13.871 21694 Z= 0.418 Chirality : 0.039 0.202 2468 Planarity : 0.005 0.047 1582 Dihedral : 33.484 174.886 4374 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 27.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: 0.60 (0.27), residues: 882 helix: 0.78 (0.19), residues: 655 sheet: None (None), residues: 0 loop : -0.48 (0.39), residues: 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.188 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2985 time to fit residues: 66.5925 Evaluate side-chains 113 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 11 optimal weight: 0.0980 chunk 17 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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 F 64 ASN H 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.052668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.040516 restraints weight = 177526.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.041074 restraints weight = 103541.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.041517 restraints weight = 69379.907| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.8544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 15000 Z= 0.253 Angle : 0.682 11.890 21694 Z= 0.397 Chirality : 0.037 0.210 2468 Planarity : 0.005 0.057 1582 Dihedral : 33.142 175.351 4374 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 22.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: 0.84 (0.27), residues: 882 helix: 0.97 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -0.42 (0.40), residues: 228 =============================================================================== Job complete usr+sys time: 2369.23 seconds wall clock time: 44 minutes 13.92 seconds (2653.92 seconds total)