Starting phenix.real_space_refine on Thu Feb 13 06:57:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iny_60712/02_2025/9iny_60712.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iny_60712/02_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_60712/02_2025/9iny_60712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iny_60712/02_2025/9iny_60712.map" model { file = "/net/cci-nas-00/data/ceres_data/9iny_60712/02_2025/9iny_60712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iny_60712/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.54, per 1000 atoms: 0.63 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: 2.17 Conformation dependent library (CDL) restraints added in 1.0 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: 0.87 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: 2.10 Time building geometry restraints manager: 2.48 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: 0.750 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.710 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.890 ------------------------------------------------------------------------------- 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 : 0.994 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: 0.1637 time to fit residues: 18.3498 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 : 0.980 ------------------------------------------------------------------------------- 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 = 9588.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102326 restraints weight = 8847.466| |-----------------------------------------------------------------------------| 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 : 0.990 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: 0.1508 time to fit residues: 13.6131 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 : 1.616 ------------------------------------------------------------------------------- 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: 0.9990 chunk 11 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.119929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106897 restraints weight = 13197.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109315 restraints weight = 8541.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111000 restraints weight = 6212.295| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8958 Z= 0.171 Angle : 0.558 6.485 12192 Z= 0.298 Chirality : 0.045 0.351 1416 Planarity : 0.003 0.030 1578 Dihedral : 5.640 44.269 1204 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.26 % Favored : 93.03 % 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: -2.38 (0.24), residues: 1119 helix: 0.05 (0.43), residues: 129 sheet: -1.15 (0.26), residues: 405 loop : -2.31 (0.22), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 169 HIS 0.002 0.000 HIS A 96 PHE 0.011 0.001 PHE B 72 TYR 0.011 0.001 TYR C 350 ARG 0.004 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 66 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 1.014 Fit side-chains REVERT: A 120 MET cc_start: 0.6671 (ptt) cc_final: 0.6086 (ptt) REVERT: B 342 ASP cc_start: 0.5885 (t0) cc_final: 0.5637 (t0) REVERT: C 210 ILE cc_start: 0.8408 (tt) cc_final: 0.8142 (tt) outliers start: 11 outliers final: 3 residues processed: 64 average time/residue: 0.1420 time to fit residues: 15.1261 Evaluate side-chains 47 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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: 0.5980 chunk 26 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 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 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 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 = 0.3737 r_free = 0.3737 target = 0.130648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.117768 restraints weight = 13559.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.120102 restraints weight = 8761.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.121765 restraints weight = 6390.614| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8958 Z= 0.266 Angle : 0.589 6.840 12192 Z= 0.313 Chirality : 0.047 0.307 1416 Planarity : 0.003 0.030 1578 Dihedral : 5.655 44.244 1204 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.13 % Favored : 91.15 % Rotamer: Outliers : 1.01 % Allowed : 10.84 % Favored : 88.15 % 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: -2.50 (0.24), residues: 1119 helix: 0.02 (0.42), residues: 129 sheet: -1.17 (0.24), residues: 459 loop : -2.55 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 144 HIS 0.005 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 52 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: B 342 ASP cc_start: 0.5672 (t0) cc_final: 0.5452 (t0) REVERT: C 210 ILE cc_start: 0.8463 (tt) cc_final: 0.8126 (tt) outliers start: 10 outliers final: 5 residues processed: 50 average time/residue: 0.1554 time to fit residues: 13.0480 Evaluate side-chains 45 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 161 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.127922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.114421 restraints weight = 13522.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.116778 restraints weight = 8782.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.118467 restraints weight = 6425.872| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8958 Z= 0.342 Angle : 0.624 6.858 12192 Z= 0.331 Chirality : 0.048 0.282 1416 Planarity : 0.003 0.029 1578 Dihedral : 5.799 44.096 1204 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.40 % Favored : 90.80 % Rotamer: Outliers : 1.72 % Allowed : 12.46 % Favored : 85.82 % 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: -0.13 (0.41), residues: 129 sheet: -1.28 (0.25), residues: 432 loop : -2.60 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 36 HIS 0.004 0.001 HIS B 113 PHE 0.012 0.002 PHE A 259 TYR 0.015 0.002 TYR B 239 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 60 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: C 210 ILE cc_start: 0.8415 (tt) cc_final: 0.8155 (tt) REVERT: C 231 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7432 (t80) outliers start: 17 outliers final: 10 residues processed: 57 average time/residue: 0.1558 time to fit residues: 14.8320 Evaluate side-chains 46 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 313 VAL 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 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 54 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 39 optimal weight: 0.0670 chunk 18 optimal weight: 0.0470 chunk 37 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.0020 ------------------------------------------------------------------------------- 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 ** 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 = 0.3787 r_free = 0.3787 target = 0.134165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.121937 restraints weight = 13414.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.124228 restraints weight = 8670.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.125829 restraints weight = 6306.191| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8958 Z= 0.164 Angle : 0.531 6.129 12192 Z= 0.282 Chirality : 0.045 0.237 1416 Planarity : 0.003 0.029 1578 Dihedral : 5.387 46.395 1204 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.80 % Allowed : 6.08 % Favored : 93.12 % Rotamer: Outliers : 1.52 % Allowed : 12.97 % Favored : 85.51 % 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: 0.28 (0.44), residues: 129 sheet: -1.15 (0.25), residues: 408 loop : -2.44 (0.22), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 169 HIS 0.002 0.001 HIS B 113 PHE 0.011 0.001 PHE B 72 TYR 0.011 0.001 TYR B 92 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 64 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 206 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8595 (t0) REVERT: A 232 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8135 (p) REVERT: C 179 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7140 (mp) REVERT: C 210 ILE cc_start: 0.8084 (tt) cc_final: 0.7774 (tt) outliers start: 15 outliers final: 6 residues processed: 63 average time/residue: 0.1507 time to fit residues: 15.7084 Evaluate side-chains 51 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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 161 ILE Chi-restraints excluded: chain C residue 179 LEU 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: 8.9990 chunk 97 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.129456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.117215 restraints weight = 13654.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118658 restraints weight = 9039.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.119356 restraints weight = 7387.258| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8958 Z= 0.288 Angle : 0.585 6.359 12192 Z= 0.310 Chirality : 0.046 0.222 1416 Planarity : 0.003 0.027 1578 Dihedral : 5.531 45.135 1204 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.31 % Favored : 90.88 % Rotamer: Outliers : 1.72 % Allowed : 13.58 % Favored : 84.70 % 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: -2.58 (0.23), residues: 1119 helix: 0.11 (0.42), residues: 129 sheet: -1.06 (0.26), residues: 396 loop : -2.67 (0.21), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 169 HIS 0.009 0.001 HIS A 113 PHE 0.011 0.002 PHE A 259 TYR 0.013 0.001 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 55 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 206 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8554 (t0) REVERT: A 232 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8185 (p) REVERT: B 232 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8142 (p) REVERT: B 277 MET cc_start: 0.8550 (tpt) cc_final: 0.7827 (tpt) REVERT: C 210 ILE cc_start: 0.8302 (tt) cc_final: 0.8004 (tt) outliers start: 17 outliers final: 10 residues processed: 50 average time/residue: 0.1528 time to fit residues: 13.1425 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 : 1.156 ------------------------------------------------------------------------------- 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 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 210 ILE 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 313 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 ** 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 = 0.3756 r_free = 0.3756 target = 0.131680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.118592 restraints weight = 13680.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.120987 restraints weight = 8759.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.122669 restraints weight = 6334.681| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2289 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= 0.202 Angle : 0.541 6.052 12192 Z= 0.286 Chirality : 0.045 0.218 1416 Planarity : 0.003 0.026 1578 Dihedral : 5.379 46.095 1204 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.89 % Allowed : 6.61 % Favored : 92.49 % Rotamer: Outliers : 1.62 % Allowed : 14.39 % Favored : 83.99 % 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: 0.28 (0.43), residues: 129 sheet: -1.22 (0.26), residues: 378 loop : -2.52 (0.21), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 169 HIS 0.003 0.001 HIS B 113 PHE 0.011 0.001 PHE B 72 TYR 0.010 0.001 TYR B 350 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 57 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 206 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8610 (t0) REVERT: A 232 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8219 (p) REVERT: A 299 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8256 (mp) REVERT: B 231 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.7343 (t80) REVERT: B 277 MET cc_start: 0.8490 (tpt) cc_final: 0.7838 (tpt) REVERT: C 210 ILE cc_start: 0.8177 (tt) cc_final: 0.7857 (tt) outliers start: 16 outliers final: 10 residues processed: 56 average time/residue: 0.1528 time to fit residues: 14.0893 Evaluate side-chains 53 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 299 LEU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 231 PHE 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 161 ILE Chi-restraints excluded: chain C residue 298 VAL 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 82 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 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 = 0.3725 r_free = 0.3725 target = 0.129350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.117148 restraints weight = 13622.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.118832 restraints weight = 8929.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.119908 restraints weight = 7118.537| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8958 Z= 0.256 Angle : 0.566 5.957 12192 Z= 0.299 Chirality : 0.045 0.215 1416 Planarity : 0.003 0.029 1578 Dihedral : 5.470 45.698 1204 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.22 % Favored : 90.88 % Rotamer: Outliers : 2.13 % Allowed : 13.98 % 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: -2.62 (0.23), residues: 1119 helix: 0.22 (0.43), residues: 129 sheet: -1.12 (0.26), residues: 375 loop : -2.67 (0.21), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 169 HIS 0.004 0.001 HIS B 113 PHE 0.010 0.001 PHE B 72 TYR 0.012 0.001 TYR B 350 ARG 0.002 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 62 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 206 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8488 (t0) REVERT: A 232 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8206 (p) REVERT: A 299 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8366 (mp) REVERT: B 231 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7498 (t80) REVERT: B 277 MET cc_start: 0.8535 (tpt) cc_final: 0.7922 (tpt) REVERT: C 210 ILE cc_start: 0.8289 (tt) cc_final: 0.7997 (tt) REVERT: C 231 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7390 (t80) outliers start: 21 outliers final: 15 residues processed: 59 average time/residue: 0.1690 time to fit residues: 16.4575 Evaluate side-chains 57 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 179 LEU 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 11 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 231 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.130870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.118731 restraints weight = 13605.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.120509 restraints weight = 8881.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.121480 restraints weight = 6997.222| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8958 Z= 0.214 Angle : 0.545 6.061 12192 Z= 0.289 Chirality : 0.045 0.210 1416 Planarity : 0.003 0.029 1578 Dihedral : 5.377 46.109 1204 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.06 % Favored : 92.05 % Rotamer: Outliers : 1.93 % Allowed : 14.29 % 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: -2.60 (0.23), residues: 1119 helix: 0.32 (0.44), residues: 129 sheet: -1.10 (0.26), residues: 396 loop : -2.73 (0.21), residues: 594 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 0.011 0.001 TYR B 350 ARG 0.003 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 56 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 206 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8474 (t0) REVERT: A 232 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8228 (p) REVERT: A 299 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8304 (mp) REVERT: B 231 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.7458 (t80) REVERT: B 277 MET cc_start: 0.8507 (tpt) cc_final: 0.7903 (tpt) REVERT: C 210 ILE cc_start: 0.8234 (tt) cc_final: 0.7911 (tt) outliers start: 19 outliers final: 13 residues processed: 54 average time/residue: 0.1460 time to fit residues: 13.3071 Evaluate side-chains 53 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 179 LEU 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 11 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 231 PHE 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 298 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 323 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 84 optimal weight: 0.1980 chunk 93 optimal weight: 9.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.103329 restraints weight = 14739.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106053 restraints weight = 9067.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.107910 restraints weight = 6459.258| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8958 Z= 0.350 Angle : 0.621 6.233 12192 Z= 0.328 Chirality : 0.047 0.210 1416 Planarity : 0.003 0.032 1578 Dihedral : 5.683 44.865 1204 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.89 % Allowed : 9.03 % Favored : 90.08 % Rotamer: Outliers : 2.33 % Allowed : 14.08 % Favored : 83.59 % 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: -2.75 (0.23), residues: 1119 helix: 0.16 (0.43), residues: 129 sheet: -1.24 (0.26), residues: 375 loop : -2.75 (0.21), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 36 HIS 0.004 0.001 HIS B 113 PHE 0.011 0.002 PHE B 353 TYR 0.016 0.001 TYR B 239 ARG 0.003 0.000 ARG B 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2088.11 seconds wall clock time: 38 minutes 45.22 seconds (2325.22 seconds total)