Starting phenix.real_space_refine on Thu Mar 13 09:07:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iny_60712/03_2025/9iny_60712.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iny_60712/03_2025/9iny_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/cci-nas-00/data/ceres_data/9iny_60712/03_2025/9iny_60712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iny_60712/03_2025/9iny_60712.map" model { file = "/net/cci-nas-00/data/ceres_data/9iny_60712/03_2025/9iny_60712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iny_60712/03_2025/9iny_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-5624/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: 5.42, per 1000 atoms: 0.62 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: 2.25 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: 0.90 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: 2.07 Time building geometry restraints manager: 2.67 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: 0.03 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.930 Find NCS groups from input model: 0.310 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: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.830 ------------------------------------------------------------------------------- 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 : 1.101 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: 0.1735 time to fit residues: 18.9829 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 : 1.019 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.113080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101309 restraints weight = 13204.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.102033 restraints weight = 9588.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102326 restraints weight = 8847.463| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 1.075 Fit side-chains REVERT: A 120 MET cc_start: 0.6759 (ptt) cc_final: 0.6112 (ptt) REVERT: B 342 ASP cc_start: 0.5890 (t0) cc_final: 0.5651 (t0) REVERT: C 120 MET cc_start: 0.6931 (ppp) cc_final: 0.6717 (ppp) REVERT: C 126 ASN cc_start: 0.8111 (t0) cc_final: 0.7887 (p0) outliers start: 13 outliers final: 8 residues processed: 54 average time/residue: 0.1470 time to fit residues: 13.5111 Evaluate side-chains 42 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 30 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 20 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.119417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.107704 restraints weight = 13187.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108784 restraints weight = 9203.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109567 restraints weight = 7891.740| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8958 Z= 0.185 Angle : 0.566 6.590 12192 Z= 0.302 Chirality : 0.046 0.357 1416 Planarity : 0.003 0.031 1578 Dihedral : 5.688 43.989 1204 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.70 % Favored : 92.58 % Rotamer: Outliers : 1.11 % Allowed : 9.02 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.24), residues: 1119 helix: -0.00 (0.42), residues: 129 sheet: -1.17 (0.26), residues: 405 loop : -2.32 (0.22), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 169 HIS 0.002 0.001 HIS A 129 PHE 0.011 0.001 PHE A 72 TYR 0.011 0.001 TYR B 350 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 63 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.967 Fit side-chains REVERT: A 120 MET cc_start: 0.6726 (ptt) cc_final: 0.6122 (ptt) REVERT: B 342 ASP cc_start: 0.5946 (t0) cc_final: 0.5685 (t0) REVERT: C 210 ILE cc_start: 0.8410 (tt) cc_final: 0.8148 (tt) outliers start: 11 outliers final: 3 residues processed: 61 average time/residue: 0.1461 time to fit residues: 14.8547 Evaluate side-chains 45 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain C residue 161 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.114668 restraints weight = 13614.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116971 restraints weight = 8979.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.118585 restraints weight = 6627.666| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8958 Z= 0.331 Angle : 0.630 7.018 12192 Z= 0.335 Chirality : 0.048 0.301 1416 Planarity : 0.003 0.033 1578 Dihedral : 5.854 43.347 1204 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.49 % Favored : 90.80 % Rotamer: Outliers : 1.32 % Allowed : 11.35 % Favored : 87.34 % 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: -0.12 (0.42), residues: 129 sheet: -1.22 (0.25), residues: 423 loop : -2.61 (0.22), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 36 HIS 0.006 0.001 HIS B 113 PHE 0.012 0.002 PHE A 259 TYR 0.016 0.002 TYR B 239 ARG 0.004 0.000 ARG B 56 *********************** 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 54 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 1.088 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 53 average time/residue: 0.1525 time to fit residues: 13.6156 Evaluate side-chains 43 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 overall best weight: 2.6784 ------------------------------------------------------------------------------- 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 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.129110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.116072 restraints weight = 13471.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.118413 restraints weight = 8831.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.120024 restraints weight = 6467.283| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8958 Z= 0.264 Angle : 0.588 6.581 12192 Z= 0.312 Chirality : 0.046 0.268 1416 Planarity : 0.003 0.030 1578 Dihedral : 5.713 44.585 1204 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.51 % Favored : 91.69 % Rotamer: Outliers : 1.52 % Allowed : 12.87 % Favored : 85.61 % 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: -2.66 (0.23), residues: 1119 helix: -0.05 (0.42), residues: 129 sheet: -1.37 (0.26), residues: 399 loop : -2.48 (0.22), residues: 591 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 0.012 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 56 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: C 231 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7383 (t80) outliers start: 15 outliers final: 10 residues processed: 53 average time/residue: 0.1496 time to fit residues: 13.4614 Evaluate side-chains 48 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 197 MET 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 298 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 39 optimal weight: 0.0020 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- 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 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.127101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.114454 restraints weight = 13538.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.115979 restraints weight = 8998.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.116852 restraints weight = 7287.980| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8958 Z= 0.314 Angle : 0.608 6.590 12192 Z= 0.322 Chirality : 0.047 0.240 1416 Planarity : 0.003 0.030 1578 Dihedral : 5.762 44.543 1204 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.67 % Favored : 90.53 % Rotamer: Outliers : 2.74 % Allowed : 12.66 % Favored : 84.60 % 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: -2.80 (0.23), residues: 1119 helix: -0.12 (0.42), residues: 129 sheet: -1.38 (0.25), residues: 423 loop : -2.70 (0.22), residues: 567 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 0.012 0.002 PHE A 259 TYR 0.013 0.001 TYR B 239 ARG 0.003 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 65 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 38 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 206 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8575 (t0) REVERT: A 232 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8059 (p) REVERT: A 299 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8389 (mp) REVERT: B 231 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7359 (t80) REVERT: B 232 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8224 (p) REVERT: C 231 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7383 (t80) outliers start: 27 outliers final: 14 residues processed: 62 average time/residue: 0.1494 time to fit residues: 15.5114 Evaluate side-chains 54 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 34 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 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 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 146 TYR 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 298 VAL 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 80 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100497 restraints weight = 14854.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.103152 restraints weight = 9218.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105002 restraints weight = 6618.197| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 8958 Z= 0.468 Angle : 0.696 6.919 12192 Z= 0.369 Chirality : 0.049 0.227 1416 Planarity : 0.004 0.033 1578 Dihedral : 6.072 43.679 1204 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.38 % Favored : 89.81 % Rotamer: Outliers : 2.43 % Allowed : 13.68 % Favored : 83.89 % 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: -2.98 (0.23), residues: 1119 helix: -0.34 (0.41), residues: 129 sheet: -1.53 (0.26), residues: 381 loop : -2.72 (0.22), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 169 HIS 0.016 0.002 HIS A 113 PHE 0.013 0.002 PHE C 259 TYR 0.021 0.002 TYR B 239 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 58 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 34 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 206 ASN cc_start: 0.9019 (OUTLIER) cc_final: 0.8759 (t0) REVERT: A 232 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8077 (p) REVERT: A 299 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8460 (mp) REVERT: B 231 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7254 (t80) REVERT: B 232 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8136 (p) REVERT: C 231 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7336 (t80) REVERT: C 342 ASP cc_start: 0.5985 (t0) cc_final: 0.5699 (t0) outliers start: 24 outliers final: 17 residues processed: 55 average time/residue: 0.1458 time to fit residues: 13.5557 Evaluate side-chains 55 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 32 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 161 ILE Chi-restraints excluded: chain A residue 206 ASN 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 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 298 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 323 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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** A 182 GLN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.123101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108151 restraints weight = 14570.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110931 restraints weight = 8771.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112859 restraints weight = 6171.835| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2423 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= 0.181 Angle : 0.546 6.113 12192 Z= 0.290 Chirality : 0.045 0.216 1416 Planarity : 0.003 0.030 1578 Dihedral : 5.537 46.957 1204 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.89 % Allowed : 6.26 % Favored : 92.85 % Rotamer: Outliers : 2.33 % Allowed : 13.98 % Favored : 83.69 % 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: 0.07 (0.43), residues: 129 sheet: -1.25 (0.26), residues: 369 loop : -2.65 (0.21), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 169 HIS 0.005 0.001 HIS A 113 PHE 0.012 0.001 PHE B 72 TYR 0.012 0.001 TYR B 92 ARG 0.003 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 70 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 47 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 206 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8668 (t0) REVERT: A 232 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8156 (p) REVERT: B 126 ASN cc_start: 0.8756 (p0) cc_final: 0.8534 (p0) REVERT: B 231 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7421 (t80) REVERT: C 210 ILE cc_start: 0.8480 (tt) cc_final: 0.8171 (tt) REVERT: C 231 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7325 (t80) outliers start: 23 outliers final: 12 residues processed: 67 average time/residue: 0.1558 time to fit residues: 16.9896 Evaluate side-chains 55 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 334 VAL 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 323 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 146 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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** ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.129804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117655 restraints weight = 13627.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.119338 restraints weight = 8860.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.120513 restraints weight = 7042.236| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2471 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= 0.218 Angle : 0.550 5.989 12192 Z= 0.291 Chirality : 0.045 0.215 1416 Planarity : 0.003 0.028 1578 Dihedral : 5.455 46.503 1204 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.69 % Favored : 91.42 % Rotamer: Outliers : 1.82 % Allowed : 14.79 % 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: -2.68 (0.23), residues: 1119 helix: 0.15 (0.43), residues: 129 sheet: -1.22 (0.26), residues: 369 loop : -2.66 (0.21), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 169 HIS 0.003 0.001 HIS B 113 PHE 0.011 0.001 PHE A 259 TYR 0.011 0.001 TYR B 350 ARG 0.003 0.000 ARG C 56 *********************** 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 60 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 206 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8658 (t0) REVERT: A 231 PHE cc_start: 0.7861 (t80) cc_final: 0.7271 (t80) REVERT: A 232 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8099 (p) REVERT: A 368 ASN cc_start: 0.7551 (OUTLIER) cc_final: 0.7099 (p0) REVERT: B 126 ASN cc_start: 0.8721 (p0) cc_final: 0.8466 (p0) REVERT: B 231 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7465 (t80) REVERT: C 210 ILE cc_start: 0.8233 (tt) cc_final: 0.7942 (tt) REVERT: C 231 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7440 (t80) outliers start: 18 outliers final: 11 residues processed: 58 average time/residue: 0.1575 time to fit residues: 15.3510 Evaluate side-chains 54 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 368 ASN 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 323 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 146 TYR 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 334 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 7.9990 chunk 104 optimal weight: 0.4980 chunk 25 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 0.0000 chunk 13 optimal weight: 6.9990 chunk 85 optimal weight: 0.4980 chunk 2 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.135278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.122654 restraints weight = 13582.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.125086 restraints weight = 8538.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.126774 restraints weight = 6114.159| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8958 Z= 0.145 Angle : 0.509 6.205 12192 Z= 0.270 Chirality : 0.044 0.202 1416 Planarity : 0.003 0.025 1578 Dihedral : 5.168 48.136 1204 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.89 % Allowed : 5.63 % Favored : 93.48 % Rotamer: Outliers : 1.11 % Allowed : 15.70 % Favored : 83.18 % 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: -2.54 (0.23), residues: 1119 helix: 0.44 (0.45), residues: 129 sheet: -1.20 (0.27), residues: 360 loop : -2.55 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS C 129 PHE 0.011 0.001 PHE B 72 TYR 0.011 0.001 TYR B 92 ARG 0.002 0.000 ARG C 56 ********************** 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 61 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 1.233 Fit side-chains REVERT: A 231 PHE cc_start: 0.7687 (t80) cc_final: 0.7235 (t80) REVERT: A 232 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8153 (p) REVERT: C 210 ILE cc_start: 0.7837 (tt) cc_final: 0.7494 (tt) outliers start: 11 outliers final: 7 residues processed: 60 average time/residue: 0.2199 time to fit residues: 21.2237 Evaluate side-chains 52 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 146 TYR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 84 optimal weight: 0.0980 chunk 93 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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** ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.131814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.119818 restraints weight = 13633.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.121559 restraints weight = 8805.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.122592 restraints weight = 6929.126| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8958 Z= 0.204 Angle : 0.539 6.066 12192 Z= 0.285 Chirality : 0.045 0.213 1416 Planarity : 0.003 0.036 1578 Dihedral : 5.230 47.204 1204 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.77 % Favored : 91.33 % Rotamer: Outliers : 1.32 % Allowed : 15.50 % Favored : 83.18 % 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: -2.56 (0.23), residues: 1119 helix: 0.46 (0.44), residues: 129 sheet: -1.21 (0.26), residues: 378 loop : -2.60 (0.21), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 169 HIS 0.005 0.001 HIS A 113 PHE 0.011 0.001 PHE B 72 TYR 0.013 0.001 TYR C 357 ARG 0.006 0.000 ARG A 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2294.36 seconds wall clock time: 42 minutes 18.08 seconds (2538.08 seconds total)