Starting phenix.real_space_refine on Sun Dec 10 09:15:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/12_2023/8g8b_29845.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/12_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_29845/12_2023/8g8b_29845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/12_2023/8g8b_29845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/12_2023/8g8b_29845.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8b_29845/12_2023/8g8b_29845.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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-1.21rc1-5172/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: 7.77, 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: 7.26 Conformation dependent library (CDL) restraints added in 1.6 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: 7.16 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: 6.34 Time building geometry restraints manager: 7.61 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: 6500 35.81 - 71.62: 1745 71.62 - 107.42: 15 107.42 - 143.23: 2 143.23 - 179.04: 1 Dihedral angle restraints: 8263 sinusoidal: 5648 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 8260 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: 0.350 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: 2.540 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 46.480 Find NCS groups from input model: 0.550 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.110 ------------------------------------------------------------------------------- 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 : 28.756 179.040 6571 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 % Allowed : 17.15 % Favored : 80.87 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP X 277 HIS 0.005 0.001 HIS B 75 PHE 0.012 0.002 PHE E 67 TYR 0.013 0.002 TYR H 80 ARG 0.004 0.000 ARG H 83 *********************** 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 : 1.175 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: 0.3548 time to fit residues: 152.0868 Evaluate side-chains 166 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2996 time to fit residues: 2.1801 ------------------------------------------------------------------------------- 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: 9.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 30.0000 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 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15000 Z= 0.268 Angle : 0.663 12.351 21694 Z= 0.389 Chirality : 0.037 0.156 2468 Planarity : 0.006 0.142 1582 Dihedral : 31.205 177.322 4762 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.13 % Allowed : 2.77 % Favored : 97.10 % 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: 1.84 (0.27), residues: 882 helix: 1.75 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -0.35 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP X 207 HIS 0.010 0.002 HIS F 75 PHE 0.020 0.002 PHE A 67 TYR 0.026 0.003 TYR H 80 ARG 0.010 0.001 ARG X 281 *********************** 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 : 1.208 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 outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.3317 time to fit residues: 100.9465 Evaluate side-chains 152 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2912 ------------------------------------------------------------------------------- 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: 4.9990 chunk 33 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 107 optimal weight: 50.0000 chunk 115 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 36 optimal weight: 30.0000 chunk 86 optimal weight: 8.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8008 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15000 Z= 0.316 Angle : 0.652 11.867 21694 Z= 0.384 Chirality : 0.036 0.163 2468 Planarity : 0.005 0.056 1582 Dihedral : 31.831 177.516 4762 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: 1.61 (0.27), residues: 882 helix: 1.55 (0.19), residues: 663 sheet: None (None), residues: 0 loop : -0.28 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 207 HIS 0.007 0.002 HIS F 75 PHE 0.018 0.002 PHE B 61 TYR 0.020 0.002 TYR A 99 ARG 0.011 0.001 ARG H 96 *********************** 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 203 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.091 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 outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.3115 time to fit residues: 87.6684 Evaluate side-chains 134 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3710 ------------------------------------------------------------------------------- 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: 9.9990 chunk 80 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 50.0000 chunk 114 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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** C 38 ASN D 64 ASN E 76 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5395 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= 0.228 Angle : 0.621 11.865 21694 Z= 0.367 Chirality : 0.035 0.145 2468 Planarity : 0.004 0.048 1582 Dihedral : 31.693 176.331 4762 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: 1.47 (0.28), residues: 882 helix: 1.43 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -0.26 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP X 207 HIS 0.006 0.001 HIS H 106 PHE 0.009 0.002 PHE G 25 TYR 0.018 0.002 TYR F 72 ARG 0.007 0.001 ARG H 96 *********************** 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 190 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.144 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 outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3159 time to fit residues: 82.7321 Evaluate side-chains 139 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3314 ------------------------------------------------------------------------------- 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: 9.9990 chunk 1 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15000 Z= 0.298 Angle : 0.662 14.236 21694 Z= 0.389 Chirality : 0.036 0.159 2468 Planarity : 0.004 0.055 1582 Dihedral : 31.972 177.086 4762 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 23.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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: 1.23 (0.27), residues: 882 helix: 1.26 (0.20), residues: 659 sheet: None (None), residues: 0 loop : -0.36 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP X 207 HIS 0.005 0.001 HIS F 75 PHE 0.016 0.002 PHE B 61 TYR 0.020 0.002 TYR X 162 ARG 0.007 0.001 ARG H 96 *********************** 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 165 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.204 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: 165 average time/residue: 0.3223 time to fit residues: 74.1293 Evaluate side-chains 118 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.107 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3761 ------------------------------------------------------------------------------- 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: 3.9990 chunk 102 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.6494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15000 Z= 0.211 Angle : 0.627 11.238 21694 Z= 0.369 Chirality : 0.035 0.145 2468 Planarity : 0.004 0.049 1582 Dihedral : 31.711 175.662 4762 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.28), residues: 882 helix: 1.39 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -0.24 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP X 207 HIS 0.008 0.001 HIS F 75 PHE 0.018 0.002 PHE F 61 TYR 0.022 0.002 TYR F 72 ARG 0.010 0.000 ARG H 96 *********************** 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 177 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.193 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: 177 average time/residue: 0.3315 time to fit residues: 81.4390 Evaluate side-chains 128 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3408 ------------------------------------------------------------------------------- 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: 0.0870 chunk 12 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 113 optimal weight: 30.0000 chunk 71 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 overall best weight: 6.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** E 68 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.7521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 15000 Z= 0.400 Angle : 0.742 18.122 21694 Z= 0.429 Chirality : 0.040 0.173 2468 Planarity : 0.005 0.047 1582 Dihedral : 32.589 176.976 4762 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 32.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 882 helix: 0.92 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -0.53 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP X 207 HIS 0.010 0.002 HIS F 75 PHE 0.018 0.002 PHE F 61 TYR 0.023 0.003 TYR F 51 ARG 0.014 0.001 ARG H 76 *********************** 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 156 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.148 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 outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.3168 time to fit residues: 68.2654 Evaluate side-chains 107 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3737 ------------------------------------------------------------------------------- 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: 0.9990 chunk 45 optimal weight: 0.0870 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 overall best weight: 0.9364 ------------------------------------------------------------------------------- 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** ** C 89 ASN ** 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: 0.8038 moved from start: 0.7353 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= 0.191 Angle : 0.650 12.787 21694 Z= 0.376 Chirality : 0.036 0.189 2468 Planarity : 0.004 0.053 1582 Dihedral : 31.613 175.303 4762 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 1.13 (0.27), residues: 882 helix: 1.17 (0.20), residues: 659 sheet: None (None), residues: 0 loop : -0.31 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 207 HIS 0.005 0.001 HIS H 79 PHE 0.028 0.002 PHE A 67 TYR 0.020 0.002 TYR F 72 ARG 0.009 0.001 ARG D 69 *********************** 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 175 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.166 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 outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.3189 time to fit residues: 76.9191 Evaluate side-chains 120 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2889 ------------------------------------------------------------------------------- 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: 5.9990 chunk 99 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.8018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 15000 Z= 0.366 Angle : 0.724 15.017 21694 Z= 0.422 Chirality : 0.039 0.211 2468 Planarity : 0.006 0.128 1582 Dihedral : 32.331 177.415 4762 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 29.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: 0.77 (0.27), residues: 882 helix: 0.93 (0.19), residues: 657 sheet: None (None), residues: 0 loop : -0.52 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP X 207 HIS 0.005 0.001 HIS F 75 PHE 0.022 0.002 PHE B 61 TYR 0.054 0.003 TYR D 80 ARG 0.017 0.001 ARG H 76 *********************** 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 162 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.111 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: 162 average time/residue: 0.3054 time to fit residues: 69.0776 Evaluate side-chains 112 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2309 ------------------------------------------------------------------------------- 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: 3.9990 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** E 68 GLN ** 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: 0.8170 moved from start: 0.8492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15000 Z= 0.332 Angle : 0.722 17.271 21694 Z= 0.415 Chirality : 0.039 0.143 2468 Planarity : 0.005 0.082 1582 Dihedral : 32.463 177.105 4762 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 26.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.65 (0.27), residues: 882 helix: 0.83 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -0.53 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP X 207 HIS 0.006 0.002 HIS D 79 PHE 0.021 0.002 PHE B 61 TYR 0.039 0.003 TYR D 80 ARG 0.009 0.001 ARG D 69 ********************** 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 159 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.121 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 outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.3188 time to fit residues: 70.3226 Evaluate side-chains 106 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4430 ------------------------------------------------------------------------------- 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: 4.9990 chunk 86 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 11 optimal weight: 0.0570 chunk 17 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 overall best weight: 4.6106 ------------------------------------------------------------------------------- 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** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.051324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.039303 restraints weight = 180587.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.039904 restraints weight = 106408.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.040289 restraints weight = 72258.382| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.8758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15000 Z= 0.312 Angle : 0.704 12.661 21694 Z= 0.410 Chirality : 0.039 0.146 2468 Planarity : 0.005 0.049 1582 Dihedral : 32.457 177.671 4762 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 26.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 0.83 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -0.65 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP X 207 HIS 0.005 0.002 HIS F 75 PHE 0.028 0.002 PHE B 61 TYR 0.028 0.003 TYR D 80 ARG 0.008 0.001 ARG X 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2486.71 seconds wall clock time: 46 minutes 13.31 seconds (2773.31 seconds total)