Starting phenix.real_space_refine on Fri Nov 15 10:38:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iny_60712/11_2024/9iny_60712.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iny_60712/11_2024/9iny_60712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iny_60712/11_2024/9iny_60712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iny_60712/11_2024/9iny_60712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iny_60712/11_2024/9iny_60712.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9iny_60712/11_2024/9iny_60712.cif" } resolution = 3.6 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= -0.005 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 24 5.16 5 C 5532 2.51 5 N 1461 2.21 5 O 1776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8793 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2931 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 13, 'TRANS': 361} Chain: "B" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2931 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 13, 'TRANS': 361} Chain: "C" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2931 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 13, 'TRANS': 361} Time building chain proxies: 5.33, per 1000 atoms: 0.61 Number of scatterers: 8793 At special positions: 0 Unit cell: (118.3, 113.1, 65, 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 24 16.00 O 1776 8.00 N 1461 7.00 C 5532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 9 sheets defined 13.8% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 91 through 100 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 192 through 202 removed outlier: 3.779A pdb=" N THR A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'B' and resid 5 through 9 removed outlier: 3.578A pdb=" N ASN B 8 " --> pdb=" O LEU B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 100 removed outlier: 3.525A pdb=" N TRP B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.522A pdb=" N ILE B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 202 removed outlier: 3.724A pdb=" N THR B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 358 through 368 Processing helix chain 'C' and resid 91 through 100 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 192 through 202 removed outlier: 3.745A pdb=" N THR C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 358 through 368 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 14 removed outlier: 4.392A pdb=" N ILE A 11 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 26 " --> pdb=" O VAL A 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 26 through 28 current: chain 'A' and resid 68 through 70 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 70 current: chain 'A' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 119 through 122 current: chain 'A' and resid 145 through 159 removed outlier: 3.935A pdb=" N GLN A 151 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER A 170 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA A 155 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N THR A 168 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL A 157 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ARG A 166 " --> pdb=" O VAL A 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 173 current: chain 'A' and resid 220 through 221 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 220 through 221 current: chain 'A' and resid 259 through 268 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 268 current: chain 'A' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 307 through 319 current: chain 'A' and resid 331 through 338 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 46 removed outlier: 7.035A pdb=" N ASN A 41 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 14 removed outlier: 4.407A pdb=" N ILE B 11 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 26 " --> pdb=" O VAL B 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 26 through 28 current: chain 'B' and resid 68 through 70 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 70 current: chain 'B' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 119 through 122 current: chain 'B' and resid 145 through 159 removed outlier: 4.204A pdb=" N GLN B 151 " --> pdb=" O ASN B 172 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER B 170 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA B 155 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N THR B 168 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL B 157 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ARG B 166 " --> pdb=" O VAL B 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 166 through 173 current: chain 'B' and resid 220 through 221 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 220 through 221 current: chain 'B' and resid 259 through 268 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 268 current: chain 'B' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 307 through 319 current: chain 'B' and resid 331 through 338 Processing sheet with id=AA5, first strand: chain 'B' and resid 40 through 46 removed outlier: 6.994A pdb=" N ASN B 41 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 14 removed outlier: 4.399A pdb=" N ILE C 11 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 26 " --> pdb=" O VAL C 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 26 through 28 current: chain 'C' and resid 68 through 70 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 70 current: chain 'C' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 119 through 122 current: chain 'C' and resid 145 through 159 removed outlier: 4.100A pdb=" N GLN C 151 " --> pdb=" O ASN C 172 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER C 170 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA C 155 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR C 168 " --> pdb=" O ALA C 155 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 167 through 173 current: chain 'C' and resid 220 through 221 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 220 through 221 current: chain 'C' and resid 259 through 268 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 268 current: chain 'C' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 307 through 319 current: chain 'C' and resid 331 through 338 Processing sheet with id=AA8, first strand: chain 'C' and resid 40 through 46 removed outlier: 6.971A pdb=" N ASN C 41 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 79 through 80 119 hydrogen bonds defined for protein. 345 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: 2.12 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1812 1.33 - 1.45: 2075 1.45 - 1.57: 5026 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 8958 Sorted by residual: bond pdb=" CA ASP C 374 " pdb=" CB ASP C 374 " ideal model delta sigma weight residual 1.534 1.494 0.040 1.64e-02 3.72e+03 5.85e+00 bond pdb=" N VAL B 376 " pdb=" CA VAL B 376 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.25e-02 6.40e+03 5.13e+00 bond pdb=" CA SER B 354 " pdb=" CB SER B 354 " ideal model delta sigma weight residual 1.534 1.498 0.036 1.65e-02 3.67e+03 4.88e+00 bond pdb=" CA VAL B 376 " pdb=" C VAL B 376 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.27e-02 6.20e+03 4.50e+00 bond pdb=" C SER B 354 " pdb=" O SER B 354 " ideal model delta sigma weight residual 1.234 1.207 0.027 1.29e-02 6.01e+03 4.44e+00 ... (remaining 8953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 11871 2.09 - 4.17: 275 4.17 - 6.26: 40 6.26 - 8.35: 4 8.35 - 10.44: 2 Bond angle restraints: 12192 Sorted by residual: angle pdb=" N ALA B 375 " pdb=" CA ALA B 375 " pdb=" C ALA B 375 " ideal model delta sigma weight residual 111.14 117.23 -6.09 1.08e+00 8.57e-01 3.18e+01 angle pdb=" N VAL B 376 " pdb=" CA VAL B 376 " pdb=" C VAL B 376 " ideal model delta sigma weight residual 109.34 119.78 -10.44 2.08e+00 2.31e-01 2.52e+01 angle pdb=" N VAL A 376 " pdb=" CA VAL A 376 " pdb=" C VAL A 376 " ideal model delta sigma weight residual 109.34 118.45 -9.11 2.08e+00 2.31e-01 1.92e+01 angle pdb=" N ALA A 375 " pdb=" CA ALA A 375 " pdb=" C ALA A 375 " ideal model delta sigma weight residual 111.14 115.67 -4.53 1.08e+00 8.57e-01 1.76e+01 angle pdb=" N VAL C 376 " pdb=" CA VAL C 376 " pdb=" C VAL C 376 " ideal model delta sigma weight residual 109.34 117.09 -7.75 2.08e+00 2.31e-01 1.39e+01 ... (remaining 12187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.68: 4604 12.68 - 25.36: 532 25.36 - 38.04: 170 38.04 - 50.72: 32 50.72 - 63.40: 8 Dihedral angle restraints: 5346 sinusoidal: 2085 harmonic: 3261 Sorted by residual: dihedral pdb=" C VAL C 376 " pdb=" N VAL C 376 " pdb=" CA VAL C 376 " pdb=" CB VAL C 376 " ideal model delta harmonic sigma weight residual -122.00 -137.61 15.61 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" C VAL B 376 " pdb=" N VAL B 376 " pdb=" CA VAL B 376 " pdb=" CB VAL B 376 " ideal model delta harmonic sigma weight residual -122.00 -136.34 14.34 0 2.50e+00 1.60e-01 3.29e+01 dihedral pdb=" CA GLY B 108 " pdb=" C GLY B 108 " pdb=" N THR B 109 " pdb=" CA THR B 109 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 5343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1301 0.098 - 0.196: 101 0.196 - 0.295: 9 0.295 - 0.393: 2 0.393 - 0.491: 3 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CA VAL C 376 " pdb=" N VAL C 376 " pdb=" C VAL C 376 " pdb=" CB VAL C 376 " both_signs ideal model delta sigma weight residual False 2.44 1.95 0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CA VAL B 376 " pdb=" N VAL B 376 " pdb=" C VAL B 376 " pdb=" CB VAL B 376 " both_signs ideal model delta sigma weight residual False 2.44 2.00 0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CA ILE B 161 " pdb=" N ILE B 161 " pdb=" C ILE B 161 " pdb=" CB ILE B 161 " both_signs ideal model delta sigma weight residual False 2.43 2.03 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 1413 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 160 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C ASP B 160 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP B 160 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE B 161 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 160 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C ASP C 160 " 0.038 2.00e-02 2.50e+03 pdb=" O ASP C 160 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE C 161 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 161 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C ILE B 161 " -0.034 2.00e-02 2.50e+03 pdb=" O ILE B 161 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU B 162 " 0.011 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 39 2.51 - 3.11: 6598 3.11 - 3.70: 12864 3.70 - 4.30: 19091 4.30 - 4.90: 32117 Nonbonded interactions: 70709 Sorted by model distance: nonbonded pdb=" O VAL A 376 " pdb=" CG1 VAL A 376 " model vdw 1.909 3.460 nonbonded pdb=" NE2 HIS C 96 " pdb=" O ARG C 102 " model vdw 2.260 3.120 nonbonded pdb=" NE2 HIS B 96 " pdb=" O ARG B 102 " model vdw 2.265 3.120 nonbonded pdb=" OE1 GLN A 151 " pdb=" OG SER A 254 " model vdw 2.288 3.040 nonbonded pdb=" OG SER B 341 " pdb=" OD2 ASP B 347 " model vdw 2.299 3.040 ... (remaining 70704 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' selection = chain 'C' } 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: 0.420 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.100 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 0.003 0.040 8958 Z= 0.226 Angle : 0.751 10.435 12192 Z= 0.442 Chirality : 0.055 0.491 1416 Planarity : 0.003 0.041 1578 Dihedral : 12.392 63.401 3252 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.24 % Favored : 92.05 % Rotamer: Outliers : 0.71 % Allowed : 0.10 % Favored : 99.19 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.25), residues: 1119 helix: 0.56 (0.46), residues: 126 sheet: -0.74 (0.26), residues: 450 loop : -2.26 (0.23), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 144 HIS 0.003 0.001 HIS B 96 PHE 0.010 0.001 PHE A 72 TYR 0.021 0.001 TYR B 357 ARG 0.006 0.001 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.5999 (ptt) cc_final: 0.5769 (ptt) REVERT: C 210 ILE cc_start: 0.8288 (tt) cc_final: 0.7982 (tt) outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.1641 time to fit residues: 18.5374 Evaluate side-chains 49 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain C residue 161 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN B 113 HIS B 115 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 8958 Z= 0.445 Angle : 0.734 7.569 12192 Z= 0.392 Chirality : 0.050 0.175 1416 Planarity : 0.004 0.037 1578 Dihedral : 6.560 56.144 1206 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.85 % Favored : 90.44 % Rotamer: Outliers : 1.32 % Allowed : 6.18 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.24), residues: 1119 helix: -0.25 (0.40), residues: 129 sheet: -0.91 (0.26), residues: 414 loop : -2.53 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 36 HIS 0.004 0.001 HIS B 96 PHE 0.016 0.002 PHE C 259 TYR 0.025 0.002 TYR B 239 ARG 0.004 0.001 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 1.066 Fit side-chains REVERT: A 120 MET cc_start: 0.6695 (ptt) cc_final: 0.6090 (ptt) REVERT: B 342 ASP cc_start: 0.5630 (t0) cc_final: 0.5424 (t0) outliers start: 13 outliers final: 8 residues processed: 54 average time/residue: 0.1476 time to fit residues: 13.6137 Evaluate side-chains 41 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 323 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN B 113 HIS ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8958 Z= 0.267 Angle : 0.607 6.779 12192 Z= 0.324 Chirality : 0.047 0.348 1416 Planarity : 0.003 0.033 1578 Dihedral : 5.888 43.127 1204 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.77 % Favored : 91.51 % Rotamer: Outliers : 1.32 % Allowed : 9.52 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.23), residues: 1119 helix: -0.16 (0.41), residues: 129 sheet: -1.20 (0.25), residues: 429 loop : -2.55 (0.22), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 169 HIS 0.002 0.001 HIS A 96 PHE 0.012 0.002 PHE B 72 TYR 0.013 0.001 TYR B 239 ARG 0.003 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 1.040 Fit side-chains REVERT: A 120 MET cc_start: 0.6660 (ptt) cc_final: 0.6113 (ptt) outliers start: 13 outliers final: 6 residues processed: 56 average time/residue: 0.1528 time to fit residues: 14.2376 Evaluate side-chains 45 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8958 Z= 0.285 Angle : 0.606 6.956 12192 Z= 0.323 Chirality : 0.047 0.318 1416 Planarity : 0.003 0.032 1578 Dihedral : 5.832 44.042 1204 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.13 % Favored : 91.15 % Rotamer: Outliers : 1.72 % Allowed : 11.14 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.23), residues: 1119 helix: -0.18 (0.42), residues: 129 sheet: -1.23 (0.26), residues: 408 loop : -2.57 (0.22), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 169 HIS 0.004 0.001 HIS B 113 PHE 0.011 0.002 PHE A 259 TYR 0.013 0.001 TYR B 239 ARG 0.003 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 1.145 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 59 average time/residue: 0.1484 time to fit residues: 14.6710 Evaluate side-chains 46 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 0.1980 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8958 Z= 0.261 Angle : 0.584 6.538 12192 Z= 0.311 Chirality : 0.046 0.267 1416 Planarity : 0.003 0.030 1578 Dihedral : 5.713 44.978 1204 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.42 % Favored : 91.78 % Rotamer: Outliers : 2.63 % Allowed : 11.96 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.23), residues: 1119 helix: -0.09 (0.42), residues: 129 sheet: -1.38 (0.26), residues: 384 loop : -2.43 (0.22), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 169 HIS 0.003 0.001 HIS B 113 PHE 0.011 0.002 PHE B 72 TYR 0.012 0.001 TYR B 350 ARG 0.005 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 206 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8518 (t0) REVERT: A 232 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.7973 (p) REVERT: B 231 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7314 (t80) REVERT: C 210 ILE cc_start: 0.8428 (tt) cc_final: 0.8073 (tt) REVERT: C 231 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.7311 (t80) outliers start: 26 outliers final: 12 residues processed: 67 average time/residue: 0.1460 time to fit residues: 16.2479 Evaluate side-chains 53 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 323 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8958 Z= 0.232 Angle : 0.565 6.401 12192 Z= 0.299 Chirality : 0.045 0.245 1416 Planarity : 0.003 0.028 1578 Dihedral : 5.610 45.320 1204 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.51 % Favored : 91.69 % Rotamer: Outliers : 2.33 % Allowed : 13.17 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.23), residues: 1119 helix: 0.04 (0.43), residues: 129 sheet: -1.32 (0.25), residues: 408 loop : -2.60 (0.22), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 169 HIS 0.003 0.001 HIS B 113 PHE 0.011 0.001 PHE B 72 TYR 0.012 0.001 TYR B 350 ARG 0.004 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 39 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 206 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8458 (t0) REVERT: A 232 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.8075 (p) REVERT: A 299 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8283 (mp) REVERT: B 231 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7439 (t80) REVERT: C 210 ILE cc_start: 0.8223 (tt) cc_final: 0.7928 (tt) REVERT: C 231 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.7336 (t80) outliers start: 23 outliers final: 16 residues processed: 59 average time/residue: 0.1455 time to fit residues: 14.4378 Evaluate side-chains 59 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 38 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 323 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 0.0060 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8958 Z= 0.186 Angle : 0.538 6.074 12192 Z= 0.285 Chirality : 0.045 0.231 1416 Planarity : 0.003 0.027 1578 Dihedral : 5.445 45.979 1204 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.89 % Allowed : 6.70 % Favored : 92.40 % Rotamer: Outliers : 1.52 % Allowed : 14.69 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.23), residues: 1119 helix: 0.22 (0.43), residues: 129 sheet: -1.35 (0.25), residues: 414 loop : -2.58 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 169 HIS 0.014 0.001 HIS A 113 PHE 0.011 0.001 PHE B 72 TYR 0.011 0.001 TYR B 350 ARG 0.003 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 232 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8068 (p) REVERT: A 299 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8177 (mp) REVERT: C 210 ILE cc_start: 0.8059 (tt) cc_final: 0.7732 (tt) REVERT: C 231 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.7335 (t80) outliers start: 15 outliers final: 10 residues processed: 61 average time/residue: 0.1437 time to fit residues: 14.7967 Evaluate side-chains 51 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 313 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.0030 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 118 ASN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** 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: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8958 Z= 0.155 Angle : 0.512 6.155 12192 Z= 0.271 Chirality : 0.044 0.223 1416 Planarity : 0.002 0.023 1578 Dihedral : 5.205 47.109 1204 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.89 % Allowed : 6.08 % Favored : 93.03 % Rotamer: Outliers : 1.42 % Allowed : 15.20 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.23), residues: 1119 helix: 0.45 (0.44), residues: 129 sheet: -1.23 (0.25), residues: 393 loop : -2.39 (0.22), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 169 HIS 0.002 0.001 HIS B 113 PHE 0.011 0.001 PHE B 72 TYR 0.010 0.001 TYR B 92 ARG 0.002 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 1.105 Fit side-chains REVERT: A 299 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8195 (mp) REVERT: C 210 ILE cc_start: 0.7829 (tt) cc_final: 0.7493 (tt) outliers start: 14 outliers final: 11 residues processed: 57 average time/residue: 0.1817 time to fit residues: 16.1490 Evaluate side-chains 51 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 313 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 8958 Z= 0.385 Angle : 0.643 6.208 12192 Z= 0.340 Chirality : 0.047 0.218 1416 Planarity : 0.004 0.031 1578 Dihedral : 5.658 44.912 1204 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.89 % Allowed : 9.47 % Favored : 89.63 % Rotamer: Outliers : 2.23 % Allowed : 14.89 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.23), residues: 1119 helix: 0.00 (0.43), residues: 129 sheet: -1.23 (0.26), residues: 381 loop : -2.66 (0.21), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 36 HIS 0.004 0.001 HIS B 113 PHE 0.013 0.002 PHE A 259 TYR 0.018 0.002 TYR B 239 ARG 0.008 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 34 time to evaluate : 0.952 Fit side-chains REVERT: A 232 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8167 (p) REVERT: A 299 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8452 (mp) REVERT: B 231 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7570 (t80) REVERT: C 210 ILE cc_start: 0.8305 (tt) cc_final: 0.8025 (tt) REVERT: C 231 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7597 (t80) outliers start: 22 outliers final: 15 residues processed: 54 average time/residue: 0.1509 time to fit residues: 13.8499 Evaluate side-chains 51 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 32 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 118 ASN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8958 Z= 0.175 Angle : 0.541 6.106 12192 Z= 0.286 Chirality : 0.044 0.212 1416 Planarity : 0.003 0.030 1578 Dihedral : 5.360 46.255 1204 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.89 % Allowed : 5.63 % Favored : 93.48 % Rotamer: Outliers : 1.62 % Allowed : 15.70 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.23), residues: 1119 helix: 0.37 (0.44), residues: 129 sheet: -1.12 (0.26), residues: 369 loop : -2.45 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 169 HIS 0.002 0.001 HIS B 113 PHE 0.011 0.001 PHE B 72 TYR 0.010 0.001 TYR B 350 ARG 0.007 0.000 ARG A 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 1.023 Fit side-chains REVERT: A 126 ASN cc_start: 0.8746 (p0) cc_final: 0.8398 (p0) REVERT: A 232 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8155 (p) REVERT: A 299 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8243 (mp) REVERT: B 277 MET cc_start: 0.8387 (tpt) cc_final: 0.7840 (tpt) REVERT: C 210 ILE cc_start: 0.8064 (tt) cc_final: 0.7757 (tt) outliers start: 16 outliers final: 12 residues processed: 55 average time/residue: 0.1500 time to fit residues: 13.8813 Evaluate side-chains 54 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.128652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.116255 restraints weight = 13578.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.117695 restraints weight = 9159.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.118506 restraints weight = 7464.192| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8958 Z= 0.295 Angle : 0.583 6.288 12192 Z= 0.307 Chirality : 0.046 0.211 1416 Planarity : 0.003 0.029 1578 Dihedral : 5.457 45.963 1204 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.85 % Favored : 90.26 % Rotamer: Outliers : 2.23 % Allowed : 15.20 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.23), residues: 1119 helix: 0.18 (0.43), residues: 129 sheet: -1.28 (0.25), residues: 411 loop : -2.66 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 169 HIS 0.003 0.001 HIS B 113 PHE 0.011 0.002 PHE A 259 TYR 0.012 0.001 TYR B 239 ARG 0.007 0.000 ARG A 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1450.04 seconds wall clock time: 27 minutes 41.64 seconds (1661.64 seconds total)