Starting phenix.real_space_refine on Sun Jul 21 07:19:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g88_29843/07_2024/8g88_29843.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g88_29843/07_2024/8g88_29843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g88_29843/07_2024/8g88_29843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g88_29843/07_2024/8g88_29843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g88_29843/07_2024/8g88_29843.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g88_29843/07_2024/8g88_29843.cif" } resolution = 4.8 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= 0.004 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 7773 2.51 5 N 2598 2.21 5 O 3271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13995 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: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 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: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3417 Classifications: {'DNA': 168} Link IDs: {'rna3p': 167} Chain: "J" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 3471 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: 8.00, per 1000 atoms: 0.57 Number of scatterers: 13995 At special positions: 0 Unit cell: (82.11, 119.14, 175.49, 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 3271 8.00 N 2598 7.00 C 7773 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: 7.49 Conformation dependent library (CDL) restraints added in 1.5 seconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1674 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 10 sheets defined 75.2% alpha, 2.5% beta 155 base pairs and 306 stacking pairs defined. Time for finding SS restraints: 7.34 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.145A 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 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 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.236A 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 122 Processing helix chain 'E' and resid 44 through 55 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: 3.829A 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 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: 4.386A 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: 4.058A 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: 7.003A 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: 6.691A 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: 7.144A 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: 6.770A 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: 6.763A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.057A 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 78 492 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 155 basepair parallelities 306 stacking parallelities Total time for adding SS restraints: 6.44 Time building geometry restraints manager: 7.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2767 1.33 - 1.45: 4835 1.45 - 1.57: 6627 1.57 - 1.69: 670 1.69 - 1.81: 28 Bond restraints: 14927 Sorted by residual: bond pdb=" C1' DC J -95 " pdb=" N1 DC J -95 " ideal model delta sigma weight residual 1.490 1.549 -0.059 3.00e-02 1.11e+03 3.88e+00 bond pdb=" O3' DC I 80 " pdb=" P DA I 81 " ideal model delta sigma weight residual 1.607 1.636 -0.029 1.50e-02 4.44e+03 3.82e+00 bond pdb=" C1' DT J -75 " pdb=" N1 DT J -75 " ideal model delta sigma weight residual 1.490 1.543 -0.053 3.00e-02 1.11e+03 3.10e+00 bond pdb=" C1' DT J -77 " pdb=" N1 DT J -77 " ideal model delta sigma weight residual 1.490 1.542 -0.052 3.00e-02 1.11e+03 3.03e+00 bond pdb=" O3' DC I 82 " pdb=" P DA I 83 " ideal model delta sigma weight residual 1.607 1.632 -0.025 1.50e-02 4.44e+03 2.85e+00 ... (remaining 14922 not shown) Histogram of bond angle deviations from ideal: 97.05 - 104.45: 1204 104.45 - 111.86: 8330 111.86 - 119.26: 4495 119.26 - 126.67: 6505 126.67 - 134.07: 1062 Bond angle restraints: 21596 Sorted by residual: angle pdb=" C4' DC I 82 " pdb=" C3' DC I 82 " pdb=" O3' DC I 82 " ideal model delta sigma weight residual 110.00 117.36 -7.36 1.50e+00 4.44e-01 2.41e+01 angle pdb=" O3' DC I 82 " pdb=" C3' DC I 82 " pdb=" C2' DC I 82 " ideal model delta sigma weight residual 111.50 104.38 7.12 1.50e+00 4.44e-01 2.25e+01 angle pdb=" O3' DT J -77 " pdb=" P DG J -76 " pdb=" O5' DG J -76 " ideal model delta sigma weight residual 104.00 97.05 6.95 1.50e+00 4.44e-01 2.15e+01 angle pdb=" O3' DT J -75 " pdb=" P DG J -74 " pdb=" O5' DG J -74 " ideal model delta sigma weight residual 104.00 97.08 6.92 1.50e+00 4.44e-01 2.13e+01 angle pdb=" O3' DG J -76 " pdb=" P DT J -75 " pdb=" O5' DT J -75 " ideal model delta sigma weight residual 104.00 97.10 6.90 1.50e+00 4.44e-01 2.12e+01 ... (remaining 21591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 6595 35.89 - 71.78: 1596 71.78 - 107.66: 18 107.66 - 143.55: 0 143.55 - 179.44: 3 Dihedral angle restraints: 8212 sinusoidal: 5626 harmonic: 2586 Sorted by residual: dihedral pdb=" C4' DT I 20 " pdb=" C3' DT I 20 " pdb=" O3' DT I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual -140.00 39.44 -179.44 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA I 81 " pdb=" C3' DA I 81 " pdb=" O3' DA I 81 " pdb=" P DC I 82 " ideal model delta sinusoidal sigma weight residual -140.00 36.15 -176.15 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 80 " pdb=" C3' DC I 80 " pdb=" O3' DC I 80 " pdb=" P DA I 81 " ideal model delta sinusoidal sigma weight residual -140.00 16.00 -156.00 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 8209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2062 0.041 - 0.082: 331 0.082 - 0.123: 51 0.123 - 0.165: 9 0.165 - 0.206: 4 Chirality restraints: 2457 Sorted by residual: chirality pdb=" C3' DC I 72 " pdb=" C4' DC I 72 " pdb=" O3' DC I 72 " pdb=" C2' DC I 72 " 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 -73 " pdb=" C4' DT J -73 " pdb=" O3' DT J -73 " pdb=" C2' DT J -73 " both_signs ideal model delta sigma weight residual False -2.66 -2.86 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" C3' DC I 74 " pdb=" C4' DC I 74 " pdb=" O3' DC I 74 " pdb=" C2' DC I 74 " both_signs ideal model delta sigma weight residual False -2.66 -2.85 0.19 2.00e-01 2.50e+01 9.14e-01 ... (remaining 2454 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO G 80 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO C 80 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS X 254 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO X 255 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO X 255 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO X 255 " -0.023 5.00e-02 4.00e+02 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2950 2.80 - 3.33: 12263 3.33 - 3.85: 28072 3.85 - 4.38: 34764 4.38 - 4.90: 46610 Nonbonded interactions: 124659 Sorted by model distance: nonbonded pdb=" O GLN X 155 " pdb=" OG1 THR X 159 " model vdw 2.277 2.440 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.288 2.440 nonbonded pdb=" NE ARG X 157 " pdb=" OE2 GLU X 188 " model vdw 2.303 2.520 nonbonded pdb=" OP2 DA I 88 " pdb=" ND2 ASN X 196 " model vdw 2.303 2.520 nonbonded pdb=" NH2 ARG X 157 " pdb=" OE1 GLU X 188 " model vdw 2.305 2.520 ... (remaining 124654 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' 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: 0.720 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.150 Process input model: 47.620 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 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 0.059 14927 Z= 0.200 Angle : 0.598 11.791 21596 Z= 0.361 Chirality : 0.033 0.206 2457 Planarity : 0.004 0.047 1569 Dihedral : 27.716 179.439 6538 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.93 % Allowed : 16.78 % Favored : 82.29 % 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: 1.45 (0.26), residues: 871 helix: 1.36 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.12 (0.38), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP X 277 HIS 0.003 0.001 HIS B 75 PHE 0.011 0.001 PHE X 187 TYR 0.010 0.001 TYR B 51 ARG 0.004 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9112 (mt) cc_final: 0.8637 (mt) REVERT: B 62 LEU cc_start: 0.8727 (mt) cc_final: 0.8335 (mt) REVERT: C 97 LEU cc_start: 0.8888 (mt) cc_final: 0.7252 (mt) REVERT: D 66 VAL cc_start: 0.8533 (t) cc_final: 0.7907 (p) REVERT: E 97 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7047 (mt-10) REVERT: E 100 LEU cc_start: 0.8604 (mt) cc_final: 0.7877 (mm) REVERT: E 130 ILE cc_start: 0.7737 (mt) cc_final: 0.7519 (mm) REVERT: F 58 LEU cc_start: 0.7487 (tp) cc_final: 0.7112 (tp) REVERT: F 62 LEU cc_start: 0.8944 (mt) cc_final: 0.7987 (mt) REVERT: F 97 LEU cc_start: 0.7684 (tp) cc_final: 0.7412 (tp) REVERT: H 70 ILE cc_start: 0.8916 (mt) cc_final: 0.8643 (mm) REVERT: H 97 LEU cc_start: 0.7747 (mt) cc_final: 0.7464 (mt) outliers start: 7 outliers final: 0 residues processed: 148 average time/residue: 0.3558 time to fit residues: 69.4793 Evaluate side-chains 62 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 106 optimal weight: 50.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 93 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 14927 Z= 0.452 Angle : 0.817 9.417 21596 Z= 0.472 Chirality : 0.044 0.198 2457 Planarity : 0.006 0.052 1569 Dihedral : 32.234 175.020 4747 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 27.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % 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: 1.76 (0.27), residues: 871 helix: 1.58 (0.19), residues: 658 sheet: None (None), residues: 0 loop : 0.03 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP X 277 HIS 0.007 0.002 HIS E 113 PHE 0.020 0.003 PHE X 278 TYR 0.017 0.002 TYR D 80 ARG 0.006 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.150 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: B 62 LEU cc_start: 0.8708 (mt) cc_final: 0.8100 (mp) REVERT: B 84 MET cc_start: 0.8620 (tpt) cc_final: 0.8113 (tpp) REVERT: D 66 VAL cc_start: 0.8408 (t) cc_final: 0.8063 (p) REVERT: E 97 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7653 (mt-10) REVERT: E 100 LEU cc_start: 0.7856 (mt) cc_final: 0.7379 (mt) REVERT: F 86 VAL cc_start: 0.9181 (t) cc_final: 0.8979 (p) REVERT: H 59 MET cc_start: 0.8122 (mmp) cc_final: 0.7529 (mmm) REVERT: H 97 LEU cc_start: 0.8464 (mt) cc_final: 0.8033 (mt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.3468 time to fit residues: 35.3011 Evaluate side-chains 38 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 14927 Z= 0.293 Angle : 0.664 8.593 21596 Z= 0.391 Chirality : 0.036 0.188 2457 Planarity : 0.005 0.046 1569 Dihedral : 32.062 173.790 4747 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: 1.89 (0.27), residues: 871 helix: 1.64 (0.19), residues: 663 sheet: None (None), residues: 0 loop : 0.17 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP X 277 HIS 0.005 0.001 HIS B 75 PHE 0.026 0.002 PHE A 104 TYR 0.013 0.002 TYR B 51 ARG 0.005 0.001 ARG X 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.069 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: B 62 LEU cc_start: 0.8752 (mt) cc_final: 0.8317 (mm) REVERT: B 84 MET cc_start: 0.8444 (tpt) cc_final: 0.7533 (tpp) REVERT: D 62 PHE cc_start: 0.6861 (t80) cc_final: 0.6298 (t80) REVERT: D 66 VAL cc_start: 0.8562 (t) cc_final: 0.8202 (p) REVERT: F 62 LEU cc_start: 0.8533 (mm) cc_final: 0.8187 (mm) REVERT: H 59 MET cc_start: 0.8085 (mmp) cc_final: 0.7465 (mmm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.3637 time to fit residues: 29.2236 Evaluate side-chains 36 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.7372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 14927 Z= 0.341 Angle : 0.698 9.472 21596 Z= 0.410 Chirality : 0.039 0.165 2457 Planarity : 0.005 0.044 1569 Dihedral : 32.529 173.034 4747 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 29.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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: 1.66 (0.27), residues: 871 helix: 1.51 (0.20), residues: 649 sheet: None (None), residues: 0 loop : 0.03 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP X 277 HIS 0.008 0.002 HIS D 106 PHE 0.019 0.002 PHE E 67 TYR 0.013 0.002 TYR F 88 ARG 0.005 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 LEU cc_start: 0.8985 (mt) cc_final: 0.8474 (mm) REVERT: B 84 MET cc_start: 0.8647 (tpt) cc_final: 0.7946 (tpp) REVERT: D 66 VAL cc_start: 0.8398 (t) cc_final: 0.8175 (p) REVERT: E 86 SER cc_start: 0.8545 (p) cc_final: 0.7983 (p) REVERT: F 62 LEU cc_start: 0.8542 (mm) cc_final: 0.8269 (mm) REVERT: H 59 MET cc_start: 0.8412 (mmp) cc_final: 0.7578 (mmm) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.3451 time to fit residues: 23.4447 Evaluate side-chains 31 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.7525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14927 Z= 0.224 Angle : 0.622 8.593 21596 Z= 0.369 Chirality : 0.035 0.162 2457 Planarity : 0.004 0.044 1569 Dihedral : 32.225 172.696 4747 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.13 % Allowed : 1.33 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.28), residues: 871 helix: 1.81 (0.20), residues: 652 sheet: None (None), residues: 0 loop : 0.06 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP X 277 HIS 0.004 0.001 HIS B 75 PHE 0.028 0.002 PHE A 104 TYR 0.027 0.002 TYR C 50 ARG 0.007 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 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: B 62 LEU cc_start: 0.9003 (mt) cc_final: 0.8395 (mp) REVERT: B 84 MET cc_start: 0.8648 (tpt) cc_final: 0.8046 (tpp) REVERT: H 59 MET cc_start: 0.8069 (mmp) cc_final: 0.7378 (mmm) outliers start: 1 outliers final: 1 residues processed: 42 average time/residue: 0.3460 time to fit residues: 20.9198 Evaluate side-chains 29 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.8219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14927 Z= 0.277 Angle : 0.645 9.337 21596 Z= 0.381 Chirality : 0.036 0.183 2457 Planarity : 0.005 0.048 1569 Dihedral : 32.300 173.738 4747 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 26.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.13 % Allowed : 1.46 % Favored : 98.40 % 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: 1.85 (0.28), residues: 871 helix: 1.71 (0.20), residues: 649 sheet: None (None), residues: 0 loop : -0.11 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP X 207 HIS 0.004 0.001 HIS E 113 PHE 0.034 0.002 PHE E 104 TYR 0.014 0.002 TYR C 50 ARG 0.004 0.001 ARG H 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 LEU cc_start: 0.9004 (mt) cc_final: 0.8468 (mp) REVERT: B 84 MET cc_start: 0.8697 (tpt) cc_final: 0.8118 (tpp) REVERT: H 59 MET cc_start: 0.8141 (mmp) cc_final: 0.7423 (mmm) outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 0.3254 time to fit residues: 19.5461 Evaluate side-chains 29 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.8649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14927 Z= 0.255 Angle : 0.638 8.972 21596 Z= 0.376 Chirality : 0.036 0.181 2457 Planarity : 0.004 0.047 1569 Dihedral : 32.275 172.998 4747 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 24.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 1.80 (0.28), residues: 871 helix: 1.66 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -0.11 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP X 207 HIS 0.005 0.001 HIS D 106 PHE 0.025 0.002 PHE E 104 TYR 0.011 0.002 TYR C 57 ARG 0.003 0.001 ARG G 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 LEU cc_start: 0.9011 (mt) cc_final: 0.8508 (mp) REVERT: B 84 MET cc_start: 0.8688 (tpt) cc_final: 0.8076 (tpp) REVERT: E 86 SER cc_start: 0.8939 (p) cc_final: 0.8354 (p) REVERT: H 59 MET cc_start: 0.8191 (mmp) cc_final: 0.7395 (mmm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.3265 time to fit residues: 18.8325 Evaluate side-chains 29 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN C 104 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.9398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 14927 Z= 0.319 Angle : 0.683 9.763 21596 Z= 0.400 Chirality : 0.038 0.197 2457 Planarity : 0.005 0.055 1569 Dihedral : 32.633 174.618 4747 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 30.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: 871 helix: 1.40 (0.20), residues: 650 sheet: None (None), residues: 0 loop : -0.36 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP X 207 HIS 0.005 0.002 HIS D 106 PHE 0.016 0.002 PHE B 61 TYR 0.011 0.002 TYR D 118 ARG 0.008 0.001 ARG H 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 LEU cc_start: 0.9069 (mt) cc_final: 0.8587 (mp) REVERT: B 84 MET cc_start: 0.8535 (tpt) cc_final: 0.7878 (tpp) REVERT: H 59 MET cc_start: 0.8197 (mmp) cc_final: 0.7443 (mmm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.3285 time to fit residues: 19.4034 Evaluate side-chains 30 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 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 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 1.0316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 14927 Z= 0.429 Angle : 0.774 11.002 21596 Z= 0.449 Chirality : 0.042 0.251 2457 Planarity : 0.006 0.049 1569 Dihedral : 33.259 174.037 4747 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 39.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: 0.66 (0.27), residues: 871 helix: 0.80 (0.20), residues: 649 sheet: None (None), residues: 0 loop : -0.38 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP X 207 HIS 0.007 0.002 HIS D 46 PHE 0.030 0.003 PHE E 104 TYR 0.016 0.002 TYR D 118 ARG 0.005 0.001 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: B 62 LEU cc_start: 0.8897 (mt) cc_final: 0.8445 (mp) REVERT: B 84 MET cc_start: 0.8442 (tpt) cc_final: 0.7749 (tpp) REVERT: E 86 SER cc_start: 0.8902 (p) cc_final: 0.8259 (p) REVERT: H 59 MET cc_start: 0.8507 (mmp) cc_final: 0.7619 (mmm) REVERT: H 91 ILE cc_start: 0.8426 (pt) cc_final: 0.8112 (pt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.3072 time to fit residues: 18.2360 Evaluate side-chains 28 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 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 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 1.0319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 14927 Z= 0.316 Angle : 0.707 9.629 21596 Z= 0.412 Chirality : 0.038 0.196 2457 Planarity : 0.005 0.050 1569 Dihedral : 33.031 174.210 4747 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 30.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.28), residues: 871 helix: 1.04 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.41 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP X 207 HIS 0.006 0.002 HIS D 46 PHE 0.015 0.002 PHE X 149 TYR 0.011 0.002 TYR D 37 ARG 0.004 0.001 ARG C 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 62 LEU cc_start: 0.8903 (mt) cc_final: 0.8469 (mp) REVERT: B 84 MET cc_start: 0.8551 (tpt) cc_final: 0.7969 (tpp) REVERT: E 86 SER cc_start: 0.8976 (p) cc_final: 0.8462 (p) REVERT: E 120 MET cc_start: 0.7940 (mtm) cc_final: 0.7489 (mpp) REVERT: H 59 MET cc_start: 0.8216 (mmp) cc_final: 0.7403 (mmm) REVERT: H 91 ILE cc_start: 0.8335 (pt) cc_final: 0.8027 (pt) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.3056 time to fit residues: 18.6138 Evaluate side-chains 29 residues out of total 751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 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 = 0.2740 r_free = 0.2740 target = 0.024435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.019120 restraints weight = 311294.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.019502 restraints weight = 204292.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.019723 restraints weight = 150271.053| |-----------------------------------------------------------------------------| r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 1.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 14927 Z= 0.411 Angle : 0.770 10.622 21596 Z= 0.446 Chirality : 0.042 0.208 2457 Planarity : 0.006 0.050 1569 Dihedral : 33.525 174.674 4747 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 38.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 0.56 (0.28), residues: 871 helix: 0.78 (0.20), residues: 645 sheet: None (None), residues: 0 loop : -0.58 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP X 207 HIS 0.008 0.002 HIS G 31 PHE 0.047 0.003 PHE E 104 TYR 0.016 0.002 TYR D 118 ARG 0.005 0.001 ARG G 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1737.54 seconds wall clock time: 32 minutes 51.87 seconds (1971.87 seconds total)