Starting phenix.real_space_refine on Thu Nov 14 08:54:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c89_16473/11_2024/8c89_16473_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c89_16473/11_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_16473/11_2024/8c89_16473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c89_16473/11_2024/8c89_16473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c89_16473/11_2024/8c89_16473_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c89_16473/11_2024/8c89_16473_neut.cif" } 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. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 5.71, per 1000 atoms: 1.12 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 - 3.00 Amino acid : True - 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: 3.05 Conformation dependent library (CDL) restraints added in 1.5 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: 0.65 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: 3.07 Time building geometry restraints manager: 2.70 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: 0.00 - 2.57: 6894 2.57 - 5.14: 210 5.14 - 7.71: 11 7.71 - 10.28: 1 10.28 - 12.85: 1 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 3.040 nonbonded pdb=" NH1 ARG C 357 " pdb=" O ILE C 358 " model vdw 2.168 3.120 nonbonded pdb=" O ALA C 475 " pdb=" N CYS H 106 " model vdw 2.198 3.120 nonbonded pdb=" NE2 GLN L 38 " pdb=" O GLU L 82 " model vdw 2.232 3.120 nonbonded pdb=" OH TYR C 473 " pdb=" O THR H 104 " model vdw 2.245 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 33.800 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 24.270 Find NCS groups from input model: 0.110 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:4.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.420 ------------------------------------------------------------------------------- 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 to be fit. 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: 0.2395 time to fit residues: 42.9006 Evaluate side-chains 138 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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: 0.8980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 16 optimal weight: 0.0040 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5232 Z= 0.222 Angle : 0.721 9.134 7117 Z= 0.372 Chirality : 0.049 0.223 797 Planarity : 0.006 0.055 912 Dihedral : 10.813 112.272 796 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.29 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % 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: -2.21 (0.32), residues: 646 helix: -1.91 (0.90), residues: 28 sheet: -0.58 (0.35), residues: 226 loop : -2.07 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 353 HIS 0.006 0.002 HIS L 191 PHE 0.017 0.002 PHE H 176 TYR 0.020 0.002 TYR C 351 ARG 0.007 0.001 ARG C 466 *********************** 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 136 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 357 ARG cc_start: 0.8984 (tpt90) cc_final: 0.8684 (tpt90) REVERT: C 418 ILE cc_start: 0.9204 (pt) cc_final: 0.8997 (pt) REVERT: C 423 TYR cc_start: 0.8861 (t80) cc_final: 0.8477 (t80) REVERT: C 429 PHE cc_start: 0.9050 (t80) cc_final: 0.8778 (t80) REVERT: C 451 TYR cc_start: 0.7084 (m-80) cc_final: 0.6726 (m-80) REVERT: C 478 LYS cc_start: 0.9234 (tmtt) cc_final: 0.8947 (tmtt) REVERT: H 38 ARG cc_start: 0.9250 (ttp80) cc_final: 0.9006 (tmm-80) REVERT: H 73 ASP cc_start: 0.9312 (t0) cc_final: 0.9053 (t0) REVERT: H 80 TYR cc_start: 0.9270 (m-80) cc_final: 0.8980 (m-80) REVERT: H 93 MET cc_start: 0.9017 (tpp) cc_final: 0.8730 (tpp) REVERT: L 86 MET cc_start: 0.8485 (tpp) cc_final: 0.8099 (tpp) REVERT: L 88 TYR cc_start: 0.8151 (m-10) cc_final: 0.7789 (m-10) REVERT: L 192 LYS cc_start: 0.8961 (tppt) cc_final: 0.8757 (tptp) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2068 time to fit residues: 35.0189 Evaluate side-chains 131 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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: 0.8980 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 505 HIS ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 5232 Z= 0.309 Angle : 0.742 8.453 7117 Z= 0.389 Chirality : 0.049 0.231 797 Planarity : 0.006 0.049 912 Dihedral : 10.700 112.377 796 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 25.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.30 % Favored : 88.39 % Rotamer: Outliers : 0.18 % Allowed : 5.31 % Favored : 94.51 % 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: -2.04 (0.33), residues: 646 helix: -2.39 (0.80), residues: 28 sheet: -0.19 (0.36), residues: 214 loop : -2.06 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 353 HIS 0.005 0.002 HIS L 191 PHE 0.013 0.002 PHE L 141 TYR 0.022 0.002 TYR C 380 ARG 0.010 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 149 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 418 ILE cc_start: 0.9280 (pt) cc_final: 0.9070 (pt) REVERT: C 423 TYR cc_start: 0.8947 (t80) cc_final: 0.8519 (t80) REVERT: C 429 PHE cc_start: 0.9117 (t80) cc_final: 0.8785 (t80) REVERT: C 451 TYR cc_start: 0.7062 (m-80) cc_final: 0.6725 (m-80) REVERT: C 457 ARG cc_start: 0.7752 (ttp80) cc_final: 0.7408 (ttp80) REVERT: H 10 GLU cc_start: 0.8444 (mp0) cc_final: 0.8202 (mp0) REVERT: H 62 GLN cc_start: 0.8912 (pm20) cc_final: 0.8690 (pm20) REVERT: H 73 ASP cc_start: 0.9379 (t0) cc_final: 0.9078 (t0) REVERT: H 80 TYR cc_start: 0.9344 (m-80) cc_final: 0.9052 (m-80) REVERT: L 37 TYR cc_start: 0.9032 (m-10) cc_final: 0.8789 (m-80) REVERT: L 86 MET cc_start: 0.8520 (tpp) cc_final: 0.8253 (tpp) REVERT: L 88 TYR cc_start: 0.8272 (m-80) cc_final: 0.7795 (m-10) REVERT: L 142 TYR cc_start: 0.8460 (t80) cc_final: 0.8155 (t80) REVERT: L 174 THR cc_start: 0.8299 (m) cc_final: 0.8026 (t) REVERT: L 192 LYS cc_start: 0.8956 (tppt) cc_final: 0.8734 (tptp) REVERT: L 201 GLN cc_start: 0.8966 (mp10) cc_final: 0.8667 (mp10) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.2560 time to fit residues: 47.4608 Evaluate side-chains 140 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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: 0.4980 chunk 43 optimal weight: 0.5980 chunk 30 optimal weight: 0.0770 chunk 6 optimal weight: 0.4980 chunk 27 optimal weight: 0.0870 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 505 HIS ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5232 Z= 0.203 Angle : 0.709 8.764 7117 Z= 0.362 Chirality : 0.049 0.230 797 Planarity : 0.006 0.053 912 Dihedral : 9.940 105.909 796 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.22 % Favored : 89.63 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % 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: -1.90 (0.33), residues: 646 helix: -2.35 (0.84), residues: 28 sheet: 0.05 (0.38), residues: 208 loop : -2.01 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.005 0.002 HIS C 519 PHE 0.013 0.002 PHE C 392 TYR 0.017 0.002 TYR L 50 ARG 0.006 0.001 ARG C 493 *********************** 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 143 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.543 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: 0.9094 (t80) cc_final: 0.8854 (t80) REVERT: C 451 TYR cc_start: 0.7028 (m-80) cc_final: 0.6674 (m-80) REVERT: C 478 LYS cc_start: 0.9179 (tmtt) cc_final: 0.8913 (tmtt) REVERT: H 10 GLU cc_start: 0.8392 (mp0) cc_final: 0.8154 (mp0) REVERT: H 73 ASP cc_start: 0.9268 (t0) cc_final: 0.8963 (t0) REVERT: H 80 TYR cc_start: 0.9316 (m-80) cc_final: 0.9053 (m-80) REVERT: H 93 MET cc_start: 0.8999 (tpp) cc_final: 0.8541 (tpp) REVERT: L 37 TYR cc_start: 0.9014 (m-10) cc_final: 0.8766 (m-80) REVERT: L 86 MET cc_start: 0.8447 (tpp) cc_final: 0.8235 (tpp) REVERT: L 88 TYR cc_start: 0.8084 (m-80) cc_final: 0.7620 (m-10) REVERT: L 142 TYR cc_start: 0.8345 (t80) cc_final: 0.8067 (t80) REVERT: L 174 THR cc_start: 0.8181 (m) cc_final: 0.7917 (t) REVERT: L 192 LYS cc_start: 0.8916 (tppt) cc_final: 0.8710 (tptp) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2094 time to fit residues: 37.1891 Evaluate side-chains 137 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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: 2.9990 chunk 0 optimal weight: 50.0000 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 20 optimal weight: 0.0980 chunk 12 optimal weight: 0.2980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5232 Z= 0.226 Angle : 0.711 8.972 7117 Z= 0.365 Chirality : 0.048 0.224 797 Planarity : 0.005 0.053 912 Dihedral : 9.723 104.469 796 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.37 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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: -1.76 (0.34), residues: 646 helix: -2.41 (0.80), residues: 28 sheet: 0.04 (0.37), residues: 217 loop : -1.88 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 353 HIS 0.004 0.001 HIS C 519 PHE 0.016 0.002 PHE C 464 TYR 0.016 0.002 TYR L 50 ARG 0.004 0.001 ARG L 55 *********************** 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 141 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 365 TYR cc_start: 0.9013 (m-80) cc_final: 0.8811 (m-80) REVERT: C 429 PHE cc_start: 0.9077 (t80) cc_final: 0.8775 (t80) REVERT: C 451 TYR cc_start: 0.7018 (m-80) cc_final: 0.6722 (m-80) REVERT: C 457 ARG cc_start: 0.7782 (ttp80) cc_final: 0.7524 (ttp80) REVERT: C 478 LYS cc_start: 0.9172 (tmtt) cc_final: 0.8963 (tmtt) REVERT: H 10 GLU cc_start: 0.8378 (mp0) cc_final: 0.8039 (mp0) REVERT: H 62 GLN cc_start: 0.8908 (pm20) cc_final: 0.8671 (pm20) REVERT: H 73 ASP cc_start: 0.9271 (t0) cc_final: 0.8966 (t0) REVERT: H 80 TYR cc_start: 0.9262 (m-80) cc_final: 0.9019 (m-80) REVERT: H 176 PHE cc_start: 0.7642 (t80) cc_final: 0.7178 (t80) REVERT: L 37 TYR cc_start: 0.9037 (m-10) cc_final: 0.8781 (m-80) REVERT: L 88 TYR cc_start: 0.8048 (m-80) cc_final: 0.7684 (m-10) REVERT: L 142 TYR cc_start: 0.8297 (t80) cc_final: 0.7957 (t80) REVERT: L 174 THR cc_start: 0.8199 (m) cc_final: 0.7965 (t) REVERT: L 192 LYS cc_start: 0.8904 (tppt) cc_final: 0.8691 (tptp) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2107 time to fit residues: 37.6196 Evaluate side-chains 135 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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: 0.5980 chunk 15 optimal weight: 0.0040 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN L 126 GLN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5232 Z= 0.290 Angle : 0.749 8.817 7117 Z= 0.389 Chirality : 0.049 0.230 797 Planarity : 0.006 0.053 912 Dihedral : 9.718 104.249 796 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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 (0.33), residues: 646 helix: -2.45 (0.78), residues: 28 sheet: -0.22 (0.36), residues: 216 loop : -1.86 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 113 HIS 0.003 0.001 HIS C 519 PHE 0.015 0.002 PHE C 456 TYR 0.021 0.002 TYR L 50 ARG 0.006 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 145 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.578 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 429 PHE cc_start: 0.9127 (t80) cc_final: 0.8851 (t80) REVERT: C 451 TYR cc_start: 0.7028 (m-80) cc_final: 0.6657 (m-80) REVERT: H 47 TRP cc_start: 0.8568 (t60) cc_final: 0.7046 (t60) REVERT: H 62 GLN cc_start: 0.8945 (pm20) cc_final: 0.8524 (pm20) REVERT: H 73 ASP cc_start: 0.9319 (t0) cc_final: 0.9000 (t0) REVERT: H 76 THR cc_start: 0.8730 (t) cc_final: 0.8521 (t) REVERT: H 80 TYR cc_start: 0.9286 (m-80) cc_final: 0.9064 (m-80) REVERT: H 93 MET cc_start: 0.8859 (tpp) cc_final: 0.8537 (tpp) REVERT: L 49 ILE cc_start: 0.7110 (mp) cc_final: 0.6845 (mp) REVERT: L 88 TYR cc_start: 0.8249 (m-80) cc_final: 0.7767 (m-10) REVERT: L 142 TYR cc_start: 0.8342 (t80) cc_final: 0.7958 (t80) REVERT: L 174 THR cc_start: 0.8199 (m) cc_final: 0.7975 (t) REVERT: L 192 LYS cc_start: 0.8887 (tppt) cc_final: 0.8644 (tptp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2057 time to fit residues: 36.9321 Evaluate side-chains 138 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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: 4.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 ASN L 126 GLN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5232 Z= 0.295 Angle : 0.756 8.853 7117 Z= 0.392 Chirality : 0.050 0.219 797 Planarity : 0.006 0.056 912 Dihedral : 9.792 105.408 796 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.68 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -2.37 (0.79), residues: 28 sheet: -0.14 (0.37), residues: 210 loop : -1.90 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 113 HIS 0.003 0.001 HIS L 191 PHE 0.021 0.002 PHE H 110 TYR 0.022 0.002 TYR L 50 ARG 0.005 0.001 ARG C 357 *********************** 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 149 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 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: symmetry clash REVERT: C 365 TYR cc_start: 0.9009 (m-80) cc_final: 0.8808 (m-80) REVERT: C 377 PHE cc_start: 0.9138 (t80) cc_final: 0.8878 (t80) REVERT: C 429 PHE cc_start: 0.9172 (t80) cc_final: 0.8888 (t80) REVERT: C 451 TYR cc_start: 0.7186 (m-80) cc_final: 0.6832 (m-80) REVERT: H 10 GLU cc_start: 0.8368 (mp0) cc_final: 0.7976 (mp0) REVERT: H 47 TRP cc_start: 0.8549 (t60) cc_final: 0.7417 (t60) REVERT: H 73 ASP cc_start: 0.9289 (t0) cc_final: 0.8903 (t0) REVERT: H 74 MET cc_start: 0.8873 (mmt) cc_final: 0.8602 (mmt) REVERT: H 76 THR cc_start: 0.8750 (t) cc_final: 0.8545 (t) REVERT: H 80 TYR cc_start: 0.9320 (m-80) cc_final: 0.9103 (m-80) REVERT: H 186 TYR cc_start: 0.9287 (m-10) cc_final: 0.9047 (m-80) REVERT: L 88 TYR cc_start: 0.8154 (m-80) cc_final: 0.7682 (m-10) REVERT: L 142 TYR cc_start: 0.8346 (t80) cc_final: 0.7925 (t80) REVERT: L 174 THR cc_start: 0.8165 (m) cc_final: 0.7834 (t) REVERT: L 192 LYS cc_start: 0.8901 (tppt) cc_final: 0.8673 (tptp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1954 time to fit residues: 36.2393 Evaluate side-chains 143 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 0.0770 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 L 32 ASN L 126 GLN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 5232 Z= 0.322 Angle : 0.796 13.575 7117 Z= 0.414 Chirality : 0.051 0.224 797 Planarity : 0.006 0.053 912 Dihedral : 9.893 104.221 796 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 25.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.15 % Favored : 88.70 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -2.06 (0.33), residues: 646 helix: -2.88 (0.69), residues: 34 sheet: -0.13 (0.37), residues: 215 loop : -2.05 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP H 36 HIS 0.005 0.001 HIS C 519 PHE 0.017 0.002 PHE L 141 TYR 0.027 0.002 TYR L 50 ARG 0.007 0.001 ARG H 38 *********************** 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 145 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.554 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: 0.9161 (t80) cc_final: 0.8936 (t80) REVERT: C 429 PHE cc_start: 0.9219 (t80) cc_final: 0.8870 (t80) REVERT: C 451 TYR cc_start: 0.7092 (m-80) cc_final: 0.6703 (m-80) REVERT: H 47 TRP cc_start: 0.8605 (t60) cc_final: 0.7435 (t60) REVERT: H 73 ASP cc_start: 0.9297 (t0) cc_final: 0.8910 (t0) REVERT: H 74 MET cc_start: 0.8894 (mmt) cc_final: 0.8629 (mmt) REVERT: H 76 THR cc_start: 0.8789 (t) cc_final: 0.8563 (t) REVERT: H 80 TYR cc_start: 0.9323 (m-80) cc_final: 0.9103 (m-80) REVERT: H 93 MET cc_start: 0.8814 (tpp) cc_final: 0.8476 (tpp) REVERT: H 186 TYR cc_start: 0.9292 (m-10) cc_final: 0.9039 (m-80) REVERT: L 88 TYR cc_start: 0.8239 (m-80) cc_final: 0.7731 (m-10) REVERT: L 142 TYR cc_start: 0.8289 (t80) cc_final: 0.7859 (t80) REVERT: L 174 THR cc_start: 0.8226 (m) cc_final: 0.7864 (t) REVERT: L 192 LYS cc_start: 0.8872 (tppt) cc_final: 0.8634 (tptp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2145 time to fit residues: 38.3998 Evaluate side-chains 140 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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: 0.8980 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 60 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 32 ASN L 126 GLN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5232 Z= 0.305 Angle : 0.781 9.244 7117 Z= 0.408 Chirality : 0.051 0.214 797 Planarity : 0.006 0.053 912 Dihedral : 9.859 102.890 796 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 25.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % 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: -2.07 (0.33), residues: 646 helix: -2.95 (0.69), residues: 34 sheet: -0.16 (0.36), residues: 216 loop : -2.04 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 353 HIS 0.005 0.001 HIS C 519 PHE 0.018 0.002 PHE L 141 TYR 0.024 0.002 TYR L 50 ARG 0.009 0.001 ARG L 55 *********************** 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 to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.571 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 377 PHE cc_start: 0.9159 (t80) cc_final: 0.8917 (t80) REVERT: C 429 PHE cc_start: 0.9218 (t80) cc_final: 0.8893 (t80) REVERT: C 451 TYR cc_start: 0.7054 (m-80) cc_final: 0.6655 (m-80) REVERT: H 10 GLU cc_start: 0.8373 (mp0) cc_final: 0.8163 (mp0) REVERT: H 36 TRP cc_start: 0.8662 (m100) cc_final: 0.8304 (m100) REVERT: H 47 TRP cc_start: 0.8590 (t60) cc_final: 0.7434 (t60) REVERT: H 62 GLN cc_start: 0.8966 (pm20) cc_final: 0.8580 (pm20) REVERT: H 73 ASP cc_start: 0.9283 (t0) cc_final: 0.8891 (t0) REVERT: H 74 MET cc_start: 0.8874 (mmt) cc_final: 0.8595 (mmt) REVERT: H 76 THR cc_start: 0.8756 (t) cc_final: 0.8505 (t) REVERT: H 93 MET cc_start: 0.8907 (tpp) cc_final: 0.8590 (tpp) REVERT: H 94 TYR cc_start: 0.8737 (m-10) cc_final: 0.8271 (m-10) REVERT: H 186 TYR cc_start: 0.9315 (m-10) cc_final: 0.9051 (m-80) REVERT: L 37 TYR cc_start: 0.8968 (m-10) cc_final: 0.8764 (m-80) REVERT: L 88 TYR cc_start: 0.8238 (m-80) cc_final: 0.7723 (m-10) REVERT: L 142 TYR cc_start: 0.8284 (t80) cc_final: 0.7836 (t80) REVERT: L 174 THR cc_start: 0.8216 (m) cc_final: 0.7868 (t) REVERT: L 192 LYS cc_start: 0.8823 (tppt) cc_final: 0.8580 (tptp) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2172 time to fit residues: 38.8628 Evaluate side-chains 144 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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: 0.9980 chunk 63 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 126 GLN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3983 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= 0.320 Angle : 0.785 9.277 7117 Z= 0.412 Chirality : 0.051 0.218 797 Planarity : 0.006 0.053 912 Dihedral : 9.921 102.753 796 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 26.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -2.08 (0.33), residues: 646 helix: -2.95 (0.70), residues: 34 sheet: -0.14 (0.36), residues: 216 loop : -2.06 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 353 HIS 0.005 0.001 HIS C 519 PHE 0.019 0.002 PHE L 141 TYR 0.025 0.002 TYR L 50 ARG 0.007 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 146 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.552 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 377 PHE cc_start: 0.9170 (t80) cc_final: 0.8932 (t80) REVERT: C 400 PHE cc_start: 0.8317 (p90) cc_final: 0.8025 (p90) REVERT: C 418 ILE cc_start: 0.9267 (pt) cc_final: 0.8992 (pt) REVERT: C 422 ASN cc_start: 0.8555 (m-40) cc_final: 0.8354 (t0) REVERT: C 423 TYR cc_start: 0.8814 (t80) cc_final: 0.8307 (t80) REVERT: C 429 PHE cc_start: 0.9231 (t80) cc_final: 0.8883 (t80) REVERT: C 436 TRP cc_start: 0.9396 (p90) cc_final: 0.8876 (p90) REVERT: C 451 TYR cc_start: 0.7040 (m-80) cc_final: 0.6641 (m-80) REVERT: C 467 ASP cc_start: 0.8812 (t0) cc_final: 0.8344 (t0) REVERT: H 36 TRP cc_start: 0.8624 (m100) cc_final: 0.8259 (m100) REVERT: H 47 TRP cc_start: 0.8622 (t60) cc_final: 0.7456 (t60) REVERT: H 62 GLN cc_start: 0.8975 (pm20) cc_final: 0.8554 (pm20) REVERT: H 73 ASP cc_start: 0.9294 (t0) cc_final: 0.8940 (t0) REVERT: H 74 MET cc_start: 0.8900 (mmt) cc_final: 0.8658 (mmt) REVERT: H 76 THR cc_start: 0.8769 (t) cc_final: 0.8540 (t) REVERT: H 93 MET cc_start: 0.8897 (tpp) cc_final: 0.8604 (tpp) REVERT: H 94 TYR cc_start: 0.8732 (m-10) cc_final: 0.8274 (m-10) REVERT: H 186 TYR cc_start: 0.9338 (m-10) cc_final: 0.9056 (m-80) REVERT: L 37 TYR cc_start: 0.8958 (m-10) cc_final: 0.8754 (m-80) REVERT: L 88 TYR cc_start: 0.8175 (m-80) cc_final: 0.7708 (m-10) REVERT: L 142 TYR cc_start: 0.8251 (t80) cc_final: 0.7836 (t80) REVERT: L 174 THR cc_start: 0.8195 (m) cc_final: 0.7855 (t) REVERT: L 192 LYS cc_start: 0.8822 (tppt) cc_final: 0.8576 (tptp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2180 time to fit residues: 39.0833 Evaluate side-chains 140 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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: 1.9990 chunk 14 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 0.0870 chunk 9 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 GLN C 506 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 126 GLN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.171402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.136616 restraints weight = 10774.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.142779 restraints weight = 6816.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.147359 restraints weight = 4700.483| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.4088 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= 0.271 Angle : 0.796 9.154 7117 Z= 0.416 Chirality : 0.051 0.215 797 Planarity : 0.006 0.053 912 Dihedral : 9.944 102.884 796 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 25.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -2.05 (0.33), residues: 646 helix: -2.84 (0.70), residues: 34 sheet: -0.02 (0.37), residues: 212 loop : -2.10 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 353 HIS 0.004 0.001 HIS C 519 PHE 0.019 0.002 PHE H 176 TYR 0.022 0.002 TYR L 50 ARG 0.007 0.001 ARG L 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2078.00 seconds wall clock time: 39 minutes 50.25 seconds (2390.25 seconds total)