Starting phenix.real_space_refine on Sun Mar 10 21:12:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c89_16473/03_2024/8c89_16473_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c89_16473/03_2024/8c89_16473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c89_16473/03_2024/8c89_16473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c89_16473/03_2024/8c89_16473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c89_16473/03_2024/8c89_16473_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c89_16473/03_2024/8c89_16473_neut.pdb" } resolution = 4.41 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= 0.009 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 3227 2.51 5 N 862 2.21 5 O 992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5106 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1687 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 13, 'TRANS': 196} Chain: "H" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1698 Classifications: {'peptide': 226} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 211} Chain: "L" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1665 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.43, per 1000 atoms: 0.67 Number of scatterers: 5106 At special positions: 0 Unit cell: (68.4, 70.965, 145.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 992 8.00 N 862 7.00 C 3227 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.04 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.05 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 1 " - " ASN C 343 " " NAG B 1 " - " ASN H 102 " Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.0 seconds 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1210 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 14 sheets defined 9.0% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.044A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 389' Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.946A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 137 through 143 removed outlier: 4.097A pdb=" N SER H 142 " --> pdb=" O LYS H 139 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY H 143 " --> pdb=" O SER H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'L' and resid 123 through 129 Processing helix chain 'L' and resid 185 through 191 Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 357 removed outlier: 3.728A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.592A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.177A pdb=" N GLU H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL H 119 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA H 97 " --> pdb=" O GLN H 35 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 46 through 47 removed outlier: 3.682A pdb=" N GLN H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA H 97 " --> pdb=" O GLN H 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AA8, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.957A pdb=" N SER H 130 " --> pdb=" O LYS H 153 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL H 191 " --> pdb=" O HIS H 174 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS H 174 " --> pdb=" O VAL H 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 161 through 164 removed outlier: 3.675A pdb=" N THR H 161 " --> pdb=" O ASN H 209 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 13 removed outlier: 5.815A pdb=" N LEU L 11 " --> pdb=" O GLU L 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'L' and resid 19 through 22 Processing sheet with id=AB3, first strand: chain 'L' and resid 46 through 47 Processing sheet with id=AB4, first strand: chain 'L' and resid 118 through 120 removed outlier: 3.568A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER L 176 " --> pdb=" O THR L 166 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER L 178 " --> pdb=" O SER L 164 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER L 164 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR L 180 " --> pdb=" O GLN L 162 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 155 through 157 removed outlier: 3.650A pdb=" N TRP L 150 " --> pdb=" O GLN L 157 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR L 194 " --> pdb=" O PHE L 211 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N HIS L 200 " --> pdb=" O SER L 205 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N SER L 205 " --> pdb=" O HIS L 200 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 833 1.32 - 1.44: 1493 1.44 - 1.57: 2876 1.57 - 1.69: 0 1.69 - 1.82: 30 Bond restraints: 5232 Sorted by residual: bond pdb=" CZ ARG L 110 " pdb=" NH2 ARG L 110 " ideal model delta sigma weight residual 1.330 1.300 0.030 1.30e-02 5.92e+03 5.15e+00 bond pdb=" CD ARG L 110 " pdb=" NE ARG L 110 " ideal model delta sigma weight residual 1.458 1.427 0.031 1.40e-02 5.10e+03 4.92e+00 bond pdb=" CA SER H 125 " pdb=" CB SER H 125 " ideal model delta sigma weight residual 1.531 1.496 0.035 1.65e-02 3.67e+03 4.53e+00 bond pdb=" CA SER H 55 " pdb=" CB SER H 55 " ideal model delta sigma weight residual 1.535 1.502 0.033 1.58e-02 4.01e+03 4.29e+00 bond pdb=" C GLU H 158 " pdb=" N PRO H 159 " ideal model delta sigma weight residual 1.332 1.358 -0.027 1.30e-02 5.92e+03 4.24e+00 ... (remaining 5227 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.81: 180 106.81 - 113.73: 2747 113.73 - 120.64: 2149 120.64 - 127.56: 2008 127.56 - 134.47: 33 Bond angle restraints: 7117 Sorted by residual: angle pdb=" CG ARG L 110 " pdb=" CD ARG L 110 " pdb=" NE ARG L 110 " ideal model delta sigma weight residual 112.00 124.85 -12.85 2.20e+00 2.07e-01 3.41e+01 angle pdb=" C SER H 123 " pdb=" N ALA H 124 " pdb=" CA ALA H 124 " ideal model delta sigma weight residual 121.70 128.82 -7.12 1.80e+00 3.09e-01 1.56e+01 angle pdb=" CA SER H 123 " pdb=" C SER H 123 " pdb=" O SER H 123 " ideal model delta sigma weight residual 121.89 117.30 4.59 1.17e+00 7.31e-01 1.54e+01 angle pdb=" C THR L 111 " pdb=" N VAL L 112 " pdb=" CA VAL L 112 " ideal model delta sigma weight residual 122.33 116.29 6.04 1.61e+00 3.86e-01 1.41e+01 angle pdb=" C THR C 333 " pdb=" CA THR C 333 " pdb=" CB THR C 333 " ideal model delta sigma weight residual 110.42 117.77 -7.35 1.99e+00 2.53e-01 1.36e+01 ... (remaining 7112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.29: 3013 24.29 - 48.58: 144 48.58 - 72.87: 17 72.87 - 97.16: 4 97.16 - 121.46: 3 Dihedral angle restraints: 3181 sinusoidal: 1288 harmonic: 1893 Sorted by residual: dihedral pdb=" CB CYS H 150 " pdb=" SG CYS H 150 " pdb=" SG CYS H 206 " pdb=" CB CYS H 206 " ideal model delta sinusoidal sigma weight residual 93.00 178.58 -85.58 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CA VAL H 34 " pdb=" C VAL H 34 " pdb=" N GLN H 35 " pdb=" CA GLN H 35 " ideal model delta harmonic sigma weight residual 180.00 141.04 38.96 0 5.00e+00 4.00e-02 6.07e+01 dihedral pdb=" CA CYS H 101 " pdb=" C CYS H 101 " pdb=" N ASN H 102 " pdb=" CA ASN H 102 " ideal model delta harmonic sigma weight residual 180.00 142.12 37.88 0 5.00e+00 4.00e-02 5.74e+01 ... (remaining 3178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 475 0.075 - 0.150: 276 0.150 - 0.224: 39 0.224 - 0.299: 5 0.299 - 0.374: 2 Chirality restraints: 797 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.60e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN H 102 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 794 not shown) Planarity restraints: 914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.181 2.00e-02 2.50e+03 1.50e-01 2.80e+02 pdb=" C7 NAG A 1 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.140 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.232 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.060 2.00e-02 2.50e+03 5.01e-02 3.14e+01 pdb=" C7 NAG B 1 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.051 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.072 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 110 " 0.368 9.50e-02 1.11e+02 1.65e-01 1.69e+01 pdb=" NE ARG L 110 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG L 110 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG L 110 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG L 110 " 0.011 2.00e-02 2.50e+03 ... (remaining 911 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 207 2.70 - 3.25: 5278 3.25 - 3.80: 8452 3.80 - 4.35: 10929 4.35 - 4.90: 17257 Nonbonded interactions: 42123 Sorted by model distance: nonbonded pdb=" OG SER H 17 " pdb=" OE1 GLU H 82 " model vdw 2.149 2.440 nonbonded pdb=" NH1 ARG C 357 " pdb=" O ILE C 358 " model vdw 2.168 2.520 nonbonded pdb=" O ALA C 475 " pdb=" N CYS H 106 " model vdw 2.198 2.520 nonbonded pdb=" NE2 GLN L 38 " pdb=" O GLU L 82 " model vdw 2.232 2.520 nonbonded pdb=" OH TYR C 473 " pdb=" O THR H 104 " model vdw 2.245 2.440 ... (remaining 42118 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.060 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: 23.060 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.610 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 0.007 0.039 5232 Z= 0.471 Angle : 1.101 12.849 7117 Z= 0.677 Chirality : 0.085 0.374 797 Planarity : 0.009 0.165 912 Dihedral : 14.363 121.455 1944 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 25.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.37 % Favored : 89.32 % Rotamer: Outliers : 0.71 % Allowed : 2.65 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.16 % Twisted Proline : 2.70 % Twisted General : 0.33 % 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: -2.47 (0.32), residues: 646 helix: -2.31 (0.83), residues: 28 sheet: -0.68 (0.36), residues: 217 loop : -2.25 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP C 353 HIS 0.007 0.002 HIS L 200 PHE 0.032 0.004 PHE H 176 TYR 0.030 0.004 TYR L 50 ARG 0.007 0.001 ARG L 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 0.562 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: C 365 TYR cc_start: 0.9052 (m-80) cc_final: 0.8842 (m-80) REVERT: C 377 PHE cc_start: 0.8966 (t80) cc_final: 0.8669 (t80) REVERT: C 418 ILE cc_start: 0.9248 (pt) cc_final: 0.9040 (pt) REVERT: C 429 PHE cc_start: 0.9101 (t80) cc_final: 0.8801 (t80) REVERT: C 451 TYR cc_start: 0.6961 (m-80) cc_final: 0.6674 (m-80) REVERT: C 478 LYS cc_start: 0.9190 (tmtt) cc_final: 0.8862 (tmtt) REVERT: H 10 GLU cc_start: 0.8489 (mp0) cc_final: 0.8243 (pm20) REVERT: H 73 ASP cc_start: 0.9360 (t0) cc_final: 0.9097 (t0) REVERT: H 80 TYR cc_start: 0.9387 (m-80) cc_final: 0.9018 (m-80) REVERT: H 93 MET cc_start: 0.8715 (tpp) cc_final: 0.8322 (tpp) REVERT: L 37 TYR cc_start: 0.8936 (m-10) cc_final: 0.8720 (m-80) REVERT: L 88 TYR cc_start: 0.8526 (m-10) cc_final: 0.8064 (m-10) outliers start: 4 outliers final: 3 residues processed: 147 average time/residue: 0.2309 time to fit residues: 41.3394 Evaluate side-chains 138 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 16 optimal weight: 0.0050 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5232 Z= 0.252 Angle : 0.733 14.266 7117 Z= 0.372 Chirality : 0.048 0.215 797 Planarity : 0.005 0.046 912 Dihedral : 10.996 111.606 796 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 27.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.46 % Favored : 88.39 % Rotamer: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.16 % Twisted Proline : 2.70 % Twisted General : 0.16 % 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: -2.30 (0.32), residues: 646 helix: -1.92 (0.87), residues: 28 sheet: -0.64 (0.35), residues: 228 loop : -2.14 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 353 HIS 0.007 0.002 HIS L 191 PHE 0.016 0.002 PHE H 156 TYR 0.018 0.002 TYR L 50 ARG 0.007 0.001 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 398 ASP cc_start: 0.7719 (p0) cc_final: 0.7429 (p0) REVERT: C 418 ILE cc_start: 0.9231 (pt) cc_final: 0.9031 (pt) REVERT: C 423 TYR cc_start: 0.8888 (t80) cc_final: 0.8558 (t80) REVERT: C 429 PHE cc_start: 0.9062 (t80) cc_final: 0.8785 (t80) REVERT: C 451 TYR cc_start: 0.7059 (m-80) cc_final: 0.6679 (m-80) REVERT: C 457 ARG cc_start: 0.8202 (ttt-90) cc_final: 0.7820 (ttp80) REVERT: C 478 LYS cc_start: 0.9156 (tmtt) cc_final: 0.8813 (tmtt) REVERT: H 10 GLU cc_start: 0.8554 (mp0) cc_final: 0.8314 (mp0) REVERT: H 62 GLN cc_start: 0.8940 (pm20) cc_final: 0.8735 (pm20) REVERT: H 73 ASP cc_start: 0.9386 (t0) cc_final: 0.9106 (t0) REVERT: H 80 TYR cc_start: 0.9277 (m-80) cc_final: 0.8969 (m-80) REVERT: L 88 TYR cc_start: 0.8144 (m-80) cc_final: 0.7728 (m-10) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2046 time to fit residues: 34.8922 Evaluate side-chains 131 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.0980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 6 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5232 Z= 0.257 Angle : 0.735 15.141 7117 Z= 0.374 Chirality : 0.049 0.218 797 Planarity : 0.005 0.047 912 Dihedral : 10.702 111.154 796 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 26.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.30 % Favored : 88.54 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.16 % Twisted Proline : 2.70 % Twisted General : 0.16 % 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: -2.02 (0.33), residues: 646 helix: -2.23 (0.83), residues: 28 sheet: -0.20 (0.37), residues: 214 loop : -2.03 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 353 HIS 0.005 0.001 HIS C 519 PHE 0.015 0.002 PHE C 456 TYR 0.018 0.002 TYR L 50 ARG 0.006 0.001 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 365 TYR cc_start: 0.9096 (m-80) cc_final: 0.8886 (m-80) REVERT: C 429 PHE cc_start: 0.9099 (t80) cc_final: 0.8799 (t80) REVERT: C 451 TYR cc_start: 0.6968 (m-80) cc_final: 0.6664 (m-80) REVERT: C 478 LYS cc_start: 0.9133 (tmtt) cc_final: 0.8793 (tmtt) REVERT: H 10 GLU cc_start: 0.8535 (mp0) cc_final: 0.8168 (mp0) REVERT: H 62 GLN cc_start: 0.8956 (pm20) cc_final: 0.8730 (pm20) REVERT: H 73 ASP cc_start: 0.9394 (t0) cc_final: 0.9084 (t0) REVERT: H 80 TYR cc_start: 0.9346 (m-80) cc_final: 0.9022 (m-80) REVERT: L 88 TYR cc_start: 0.8279 (m-80) cc_final: 0.7782 (m-10) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1970 time to fit residues: 34.4166 Evaluate side-chains 134 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.1980 chunk 43 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 6 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.0070 chunk 58 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 51 optimal weight: 0.3980 overall best weight: 0.1736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 GLN L 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5232 Z= 0.181 Angle : 0.699 13.730 7117 Z= 0.348 Chirality : 0.047 0.217 797 Planarity : 0.005 0.053 912 Dihedral : 10.015 105.661 796 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.22 % Favored : 89.63 % Rotamer: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.16 % Twisted Proline : 2.70 % Twisted General : 0.16 % 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: -1.95 (0.33), residues: 646 helix: -2.18 (0.84), residues: 28 sheet: -0.23 (0.36), residues: 225 loop : -1.98 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.003 0.001 HIS C 519 PHE 0.014 0.001 PHE H 110 TYR 0.014 0.001 TYR L 50 ARG 0.005 0.001 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 365 TYR cc_start: 0.8971 (m-80) cc_final: 0.8759 (m-80) REVERT: C 398 ASP cc_start: 0.7773 (p0) cc_final: 0.7520 (p0) REVERT: C 429 PHE cc_start: 0.9079 (t80) cc_final: 0.8807 (t80) REVERT: C 451 TYR cc_start: 0.6907 (m-80) cc_final: 0.6629 (m-80) REVERT: C 457 ARG cc_start: 0.8065 (ttt-90) cc_final: 0.7764 (ttp80) REVERT: H 10 GLU cc_start: 0.8471 (mp0) cc_final: 0.8071 (mp0) REVERT: H 73 ASP cc_start: 0.9351 (t0) cc_final: 0.9035 (t0) REVERT: H 80 TYR cc_start: 0.9312 (m-80) cc_final: 0.9021 (m-80) REVERT: H 93 MET cc_start: 0.8963 (tpp) cc_final: 0.8679 (tpp) REVERT: L 37 TYR cc_start: 0.8954 (m-10) cc_final: 0.8720 (m-80) REVERT: L 88 TYR cc_start: 0.8083 (m-80) cc_final: 0.7601 (m-10) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1989 time to fit residues: 34.5908 Evaluate side-chains 129 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 50.0000 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 55 optimal weight: 0.0470 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 43 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 GLN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5232 Z= 0.302 Angle : 0.762 13.641 7117 Z= 0.390 Chirality : 0.049 0.205 797 Planarity : 0.006 0.052 912 Dihedral : 10.247 108.962 796 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 31.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.85 % Favored : 87.00 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.34), residues: 646 helix: -2.13 (0.83), residues: 28 sheet: -0.10 (0.37), residues: 213 loop : -1.92 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 353 HIS 0.003 0.001 HIS L 191 PHE 0.023 0.002 PHE C 515 TYR 0.019 0.002 TYR L 50 ARG 0.008 0.001 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 429 PHE cc_start: 0.9093 (t80) cc_final: 0.8762 (t80) REVERT: H 10 GLU cc_start: 0.8440 (mp0) cc_final: 0.8077 (mp0) REVERT: H 62 GLN cc_start: 0.8986 (pm20) cc_final: 0.8632 (pm20) REVERT: H 73 ASP cc_start: 0.9383 (t0) cc_final: 0.9089 (t0) REVERT: H 80 TYR cc_start: 0.9337 (m-80) cc_final: 0.9071 (m-80) REVERT: H 90 ASP cc_start: 0.8826 (m-30) cc_final: 0.8478 (m-30) REVERT: L 37 TYR cc_start: 0.9034 (m-10) cc_final: 0.8804 (m-80) REVERT: L 49 ILE cc_start: 0.7020 (mp) cc_final: 0.6776 (mp) REVERT: L 88 TYR cc_start: 0.8241 (m-80) cc_final: 0.7827 (m-10) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2029 time to fit residues: 36.5796 Evaluate side-chains 135 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 GLN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5232 Z= 0.298 Angle : 0.747 9.370 7117 Z= 0.385 Chirality : 0.049 0.210 797 Planarity : 0.006 0.053 912 Dihedral : 10.125 108.537 796 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 30.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.33), residues: 646 helix: -2.07 (0.83), residues: 28 sheet: -0.23 (0.37), residues: 216 loop : -1.93 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 353 HIS 0.003 0.001 HIS L 191 PHE 0.012 0.002 PHE C 429 TYR 0.022 0.002 TYR L 50 ARG 0.011 0.001 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.551 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: C 400 PHE cc_start: 0.8357 (p90) cc_final: 0.8135 (p90) REVERT: C 429 PHE cc_start: 0.9157 (t80) cc_final: 0.8868 (t80) REVERT: C 451 TYR cc_start: 0.7017 (m-80) cc_final: 0.6690 (m-80) REVERT: H 10 GLU cc_start: 0.8458 (mp0) cc_final: 0.8019 (mp0) REVERT: H 62 GLN cc_start: 0.8966 (pm20) cc_final: 0.8595 (pm20) REVERT: H 73 ASP cc_start: 0.9362 (t0) cc_final: 0.9022 (t0) REVERT: H 74 MET cc_start: 0.8972 (mmt) cc_final: 0.8710 (mmt) REVERT: H 80 TYR cc_start: 0.9310 (m-80) cc_final: 0.9050 (m-80) REVERT: H 90 ASP cc_start: 0.8824 (m-30) cc_final: 0.8447 (m-30) REVERT: H 224 LYS cc_start: 0.6088 (ptpt) cc_final: 0.5854 (ptpt) REVERT: L 88 TYR cc_start: 0.8271 (m-80) cc_final: 0.7764 (m-10) REVERT: L 142 TYR cc_start: 0.8525 (t80) cc_final: 0.8234 (t80) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1954 time to fit residues: 33.8745 Evaluate side-chains 131 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 126 GLN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 5232 Z= 0.331 Angle : 0.771 9.812 7117 Z= 0.402 Chirality : 0.049 0.222 797 Planarity : 0.006 0.052 912 Dihedral : 10.199 108.255 796 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 32.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.02 (0.33), residues: 646 helix: -2.56 (0.72), residues: 34 sheet: -0.22 (0.37), residues: 216 loop : -1.98 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP H 113 HIS 0.002 0.001 HIS C 519 PHE 0.018 0.002 PHE H 110 TYR 0.023 0.002 TYR L 50 ARG 0.006 0.001 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 377 PHE cc_start: 0.9145 (t80) cc_final: 0.8929 (t80) REVERT: C 392 PHE cc_start: 0.8257 (m-10) cc_final: 0.8041 (m-10) REVERT: C 400 PHE cc_start: 0.8360 (p90) cc_final: 0.8105 (p90) REVERT: C 418 ILE cc_start: 0.9278 (pt) cc_final: 0.9031 (pt) REVERT: C 429 PHE cc_start: 0.9190 (t80) cc_final: 0.8854 (t80) REVERT: C 451 TYR cc_start: 0.7030 (m-80) cc_final: 0.6678 (m-80) REVERT: H 62 GLN cc_start: 0.8970 (pm20) cc_final: 0.8532 (pm20) REVERT: H 73 ASP cc_start: 0.9362 (t0) cc_final: 0.9026 (t0) REVERT: H 74 MET cc_start: 0.8991 (mmt) cc_final: 0.8733 (mmt) REVERT: H 76 THR cc_start: 0.8967 (t) cc_final: 0.8749 (t) REVERT: H 80 TYR cc_start: 0.9329 (m-80) cc_final: 0.9066 (m-80) REVERT: H 224 LYS cc_start: 0.6295 (ptpt) cc_final: 0.6071 (ptpt) REVERT: L 88 TYR cc_start: 0.8331 (m-80) cc_final: 0.7815 (m-10) REVERT: L 142 TYR cc_start: 0.8535 (t80) cc_final: 0.8242 (t80) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2149 time to fit residues: 38.4476 Evaluate side-chains 136 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 5232 Z= 0.305 Angle : 0.781 9.441 7117 Z= 0.403 Chirality : 0.050 0.229 797 Planarity : 0.006 0.053 912 Dihedral : 10.192 107.636 796 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 31.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.99 (0.33), residues: 646 helix: -2.05 (0.77), residues: 34 sheet: -0.14 (0.37), residues: 213 loop : -2.03 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 113 HIS 0.005 0.001 HIS C 519 PHE 0.013 0.002 PHE H 27 TYR 0.021 0.002 TYR L 50 ARG 0.007 0.001 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.575 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: C 392 PHE cc_start: 0.8331 (m-10) cc_final: 0.8095 (m-10) REVERT: C 400 PHE cc_start: 0.8413 (p90) cc_final: 0.8144 (p90) REVERT: C 418 ILE cc_start: 0.9232 (pt) cc_final: 0.8970 (pt) REVERT: C 423 TYR cc_start: 0.8768 (t80) cc_final: 0.8251 (t80) REVERT: C 429 PHE cc_start: 0.9209 (t80) cc_final: 0.8891 (t80) REVERT: C 451 TYR cc_start: 0.7014 (m-80) cc_final: 0.6670 (m-80) REVERT: C 478 LYS cc_start: 0.9067 (tmtt) cc_final: 0.8850 (tmtt) REVERT: H 73 ASP cc_start: 0.9361 (t0) cc_final: 0.9065 (t0) REVERT: H 74 MET cc_start: 0.8988 (mmt) cc_final: 0.8731 (mmt) REVERT: H 93 MET cc_start: 0.8909 (tpp) cc_final: 0.8565 (tpp) REVERT: H 224 LYS cc_start: 0.6415 (ptpt) cc_final: 0.6127 (ptpt) REVERT: L 88 TYR cc_start: 0.8256 (m-80) cc_final: 0.7864 (m-10) REVERT: L 142 TYR cc_start: 0.8491 (t80) cc_final: 0.8192 (t80) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2118 time to fit residues: 37.9106 Evaluate side-chains 135 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5232 Z= 0.271 Angle : 0.757 8.892 7117 Z= 0.391 Chirality : 0.049 0.237 797 Planarity : 0.006 0.052 912 Dihedral : 9.940 104.863 796 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 29.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.34), residues: 646 helix: -2.07 (0.78), residues: 34 sheet: -0.18 (0.37), residues: 215 loop : -1.91 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 113 HIS 0.004 0.001 HIS C 519 PHE 0.014 0.002 PHE C 429 TYR 0.020 0.002 TYR L 50 ARG 0.010 0.001 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 377 PHE cc_start: 0.9234 (t80) cc_final: 0.8734 (t80) REVERT: C 392 PHE cc_start: 0.8312 (m-10) cc_final: 0.8084 (m-10) REVERT: C 400 PHE cc_start: 0.8438 (p90) cc_final: 0.8122 (p90) REVERT: C 418 ILE cc_start: 0.9209 (pt) cc_final: 0.8977 (pt) REVERT: C 423 TYR cc_start: 0.8790 (t80) cc_final: 0.8339 (t80) REVERT: C 429 PHE cc_start: 0.9197 (t80) cc_final: 0.8889 (t80) REVERT: C 451 TYR cc_start: 0.6942 (m-80) cc_final: 0.6621 (m-80) REVERT: H 10 GLU cc_start: 0.8362 (mp0) cc_final: 0.7982 (mp0) REVERT: H 36 TRP cc_start: 0.8800 (m100) cc_final: 0.8565 (m100) REVERT: H 47 TRP cc_start: 0.8653 (t60) cc_final: 0.7397 (t60) REVERT: H 94 TYR cc_start: 0.8953 (m-10) cc_final: 0.8497 (m-10) REVERT: H 224 LYS cc_start: 0.6463 (ptpt) cc_final: 0.6156 (ptpt) REVERT: L 37 TYR cc_start: 0.8897 (m-10) cc_final: 0.8673 (m-80) REVERT: L 88 TYR cc_start: 0.8194 (m-80) cc_final: 0.7734 (m-10) REVERT: L 142 TYR cc_start: 0.8412 (t80) cc_final: 0.8107 (t80) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2017 time to fit residues: 37.2617 Evaluate side-chains 137 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 0.3980 chunk 58 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5232 Z= 0.248 Angle : 0.773 8.651 7117 Z= 0.398 Chirality : 0.050 0.220 797 Planarity : 0.006 0.052 912 Dihedral : 10.080 106.145 796 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 28.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.92 (0.34), residues: 646 helix: -2.10 (0.77), residues: 34 sheet: -0.06 (0.37), residues: 213 loop : -1.99 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 113 HIS 0.004 0.001 HIS C 519 PHE 0.016 0.002 PHE H 176 TYR 0.022 0.002 TYR L 50 ARG 0.009 0.001 ARG L 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.512 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: C 377 PHE cc_start: 0.9158 (t80) cc_final: 0.8686 (t80) REVERT: C 400 PHE cc_start: 0.8436 (p90) cc_final: 0.8142 (p90) REVERT: C 418 ILE cc_start: 0.9197 (pt) cc_final: 0.8960 (pt) REVERT: C 423 TYR cc_start: 0.8750 (t80) cc_final: 0.8290 (t80) REVERT: C 429 PHE cc_start: 0.9205 (t80) cc_final: 0.8889 (t80) REVERT: C 451 TYR cc_start: 0.6931 (m-80) cc_final: 0.6647 (m-80) REVERT: H 10 GLU cc_start: 0.8371 (mp0) cc_final: 0.7999 (mp0) REVERT: H 47 TRP cc_start: 0.8605 (t60) cc_final: 0.7485 (t60) REVERT: H 62 GLN cc_start: 0.8972 (pm20) cc_final: 0.8532 (pm20) REVERT: H 74 MET cc_start: 0.8935 (mmt) cc_final: 0.8710 (mmt) REVERT: H 224 LYS cc_start: 0.6455 (ptpt) cc_final: 0.6110 (ptpt) REVERT: L 37 TYR cc_start: 0.8888 (m-10) cc_final: 0.8678 (m-80) REVERT: L 88 TYR cc_start: 0.8104 (m-80) cc_final: 0.7767 (m-10) REVERT: L 142 TYR cc_start: 0.8384 (t80) cc_final: 0.8084 (t80) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2071 time to fit residues: 35.4582 Evaluate side-chains 134 residues out of total 565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.167903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.133948 restraints weight = 10968.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.140353 restraints weight = 6775.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.144874 restraints weight = 4570.339| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5232 Z= 0.296 Angle : 0.779 8.195 7117 Z= 0.406 Chirality : 0.050 0.221 797 Planarity : 0.006 0.053 912 Dihedral : 10.225 107.550 796 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 33.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.93 % Favored : 86.07 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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 (0.34), residues: 646 helix: -2.12 (0.78), residues: 34 sheet: -0.29 (0.37), residues: 219 loop : -2.00 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 113 HIS 0.004 0.001 HIS C 519 PHE 0.016 0.002 PHE H 176 TYR 0.022 0.002 TYR L 50 ARG 0.012 0.001 ARG C 493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2030.94 seconds wall clock time: 37 minutes 35.27 seconds (2255.27 seconds total)