Starting phenix.real_space_refine on Sat Dec 28 13:30:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b71_15895/12_2024/8b71_15895.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b71_15895/12_2024/8b71_15895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b71_15895/12_2024/8b71_15895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b71_15895/12_2024/8b71_15895.map" model { file = "/net/cci-nas-00/data/ceres_data/8b71_15895/12_2024/8b71_15895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b71_15895/12_2024/8b71_15895.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 34 5.16 5 C 5766 2.51 5 N 1406 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8694 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4303 Classifications: {'peptide': 552} Link IDs: {'PTRANS': 23, 'TRANS': 528} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Classifications: {'RNA': 1} Restraints were copied for chains: B Time building chain proxies: 7.82, per 1000 atoms: 0.90 Number of scatterers: 8694 At special positions: 0 Unit cell: (113.847, 88.917, 98.889, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 4 15.00 O 1484 8.00 N 1406 7.00 C 5766 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: 2.60 Conformation dependent library (CDL) restraints added in 1.0 seconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 1 sheets defined 78.2% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 30 through 40 removed outlier: 6.235A pdb=" N ASP A 36 " --> pdb=" O MET A 32 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ALA A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 53 removed outlier: 4.435A pdb=" N THR A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLU A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.651A pdb=" N TRP A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 88 Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.631A pdb=" N ASN A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 137 Processing helix chain 'A' and resid 138 through 142 removed outlier: 4.219A pdb=" N ASP A 142 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 3.814A pdb=" N ILE A 147 " --> pdb=" O TYR A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 170 removed outlier: 3.670A pdb=" N LEU A 170 " --> pdb=" O ALA A 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 167 through 170' Processing helix chain 'A' and resid 171 through 193 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 228 through 229 No H-bonds generated for 'chain 'A' and resid 228 through 229' Processing helix chain 'A' and resid 230 through 231 No H-bonds generated for 'chain 'A' and resid 230 through 231' Processing helix chain 'A' and resid 232 through 238 removed outlier: 4.220A pdb=" N SER A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 245 through 276 Processing helix chain 'A' and resid 284 through 295 Processing helix chain 'A' and resid 297 through 331 Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 347 through 365 Processing helix chain 'A' and resid 369 through 399 Proline residue: A 375 - end of helix Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 403 through 429 Processing helix chain 'A' and resid 429 through 463 Proline residue: A 435 - end of helix Proline residue: A 441 - end of helix removed outlier: 4.398A pdb=" N ILE A 463 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 498 Processing helix chain 'A' and resid 509 through 523 Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 582 through 591 removed outlier: 3.887A pdb=" N LEU A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 40 removed outlier: 6.235A pdb=" N ASP B 36 " --> pdb=" O MET B 32 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ALA B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 4.434A pdb=" N THR B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLU B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.651A pdb=" N TRP B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 88 Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.631A pdb=" N ASN B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 137 Processing helix chain 'B' and resid 138 through 142 removed outlier: 4.220A pdb=" N ASP B 142 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 removed outlier: 3.814A pdb=" N ILE B 147 " --> pdb=" O TYR B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 170 removed outlier: 3.670A pdb=" N LEU B 170 " --> pdb=" O ALA B 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 167 through 170' Processing helix chain 'B' and resid 171 through 193 Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 228 through 229 No H-bonds generated for 'chain 'B' and resid 228 through 229' Processing helix chain 'B' and resid 230 through 231 No H-bonds generated for 'chain 'B' and resid 230 through 231' Processing helix chain 'B' and resid 232 through 238 removed outlier: 4.220A pdb=" N SER B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 245 through 276 Processing helix chain 'B' and resid 284 through 295 Processing helix chain 'B' and resid 297 through 331 Proline residue: B 323 - end of helix Processing helix chain 'B' and resid 336 through 340 Processing helix chain 'B' and resid 347 through 365 Processing helix chain 'B' and resid 369 through 399 Proline residue: B 375 - end of helix Proline residue: B 384 - end of helix Processing helix chain 'B' and resid 403 through 429 Processing helix chain 'B' and resid 429 through 463 Proline residue: B 435 - end of helix Proline residue: B 441 - end of helix removed outlier: 4.398A pdb=" N ILE B 463 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 498 Processing helix chain 'B' and resid 509 through 523 Processing helix chain 'B' and resid 540 through 557 Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.888A pdb=" N LEU B 586 " --> pdb=" O SER B 582 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 591 " --> pdb=" O ARG B 587 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 529 through 533 removed outlier: 3.633A pdb=" N VAL A 504 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 561 " --> pdb=" O MET A 597 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ALA A 599 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL A 563 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 600 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 600 " --> pdb=" O VAL B 598 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL B 561 " --> pdb=" O MET B 597 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ALA B 599 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL B 563 " --> pdb=" O ALA B 599 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 504 " --> pdb=" O VAL B 478 " (cutoff:3.500A) 631 hydrogen bonds defined for protein. 1857 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: 2.79 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2593 1.34 - 1.46: 1744 1.46 - 1.57: 4503 1.57 - 1.69: 8 1.69 - 1.81: 62 Bond restraints: 8910 Sorted by residual: bond pdb="C3'1 2BA A1001 " pdb="O3'1 2BA A1001 " ideal model delta sigma weight residual 1.418 1.344 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb="C3'1 2BA B 901 " pdb="O3'1 2BA B 901 " ideal model delta sigma weight residual 1.418 1.345 0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C5' 2BA A1001 " pdb=" O5' 2BA A1001 " ideal model delta sigma weight residual 1.433 1.365 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C5' 2BA B 901 " pdb=" O5' 2BA B 901 " ideal model delta sigma weight residual 1.433 1.365 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C3' 2BA B 901 " pdb=" O3' 2BA B 901 " ideal model delta sigma weight residual 1.410 1.352 0.058 2.00e-02 2.50e+03 8.54e+00 ... (remaining 8905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 11773 1.71 - 3.41: 261 3.41 - 5.12: 67 5.12 - 6.82: 23 6.82 - 8.53: 6 Bond angle restraints: 12130 Sorted by residual: angle pdb=" C2' 2BA A1001 " pdb=" C3' 2BA A1001 " pdb=" O3' 2BA A1001 " ideal model delta sigma weight residual 117.41 108.88 8.53 3.00e+00 1.11e-01 8.08e+00 angle pdb=" C2' 2BA B 901 " pdb=" C3' 2BA B 901 " pdb=" O3' 2BA B 901 " ideal model delta sigma weight residual 117.41 108.91 8.50 3.00e+00 1.11e-01 8.03e+00 angle pdb=" O1P 2BA A1001 " pdb=" P 2BA A1001 " pdb=" O2P 2BA A1001 " ideal model delta sigma weight residual 121.18 129.06 -7.88 3.00e+00 1.11e-01 6.89e+00 angle pdb=" O1P 2BA B 901 " pdb=" P 2BA B 901 " pdb=" O2P 2BA B 901 " ideal model delta sigma weight residual 121.18 128.98 -7.80 3.00e+00 1.11e-01 6.77e+00 angle pdb=" C LYS A 572 " pdb=" N ARG A 573 " pdb=" CA ARG A 573 " ideal model delta sigma weight residual 121.54 126.46 -4.92 1.91e+00 2.74e-01 6.63e+00 ... (remaining 12125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.65: 5170 34.65 - 69.31: 110 69.31 - 103.96: 14 103.96 - 138.61: 2 138.61 - 173.26: 8 Dihedral angle restraints: 5304 sinusoidal: 2102 harmonic: 3202 Sorted by residual: dihedral pdb=" C5' 2BA B 901 " pdb=" O5' 2BA B 901 " pdb=" P 2BA B 901 " pdb=" O1P 2BA B 901 " ideal model delta sinusoidal sigma weight residual 191.97 18.71 173.26 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C5' 2BA A1001 " pdb=" O5' 2BA A1001 " pdb=" P 2BA A1001 " pdb=" O1P 2BA A1001 " ideal model delta sinusoidal sigma weight residual 191.97 18.79 173.18 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb="C5'1 2BA B 901 " pdb=" P1 2BA B 901 " pdb="O5'1 2BA B 901 " pdb="O2P1 2BA B 901 " ideal model delta sinusoidal sigma weight residual 30.08 -142.04 172.12 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 5301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1251 0.062 - 0.124: 187 0.124 - 0.186: 14 0.186 - 0.248: 0 0.248 - 0.310: 2 Chirality restraints: 1454 Sorted by residual: chirality pdb=" C4' 2BA B 901 " pdb=" C3' 2BA B 901 " pdb=" C5' 2BA B 901 " pdb=" O4' 2BA B 901 " both_signs ideal model delta sigma weight residual False -2.39 -2.70 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C4' 2BA A1001 " pdb=" C3' 2BA A1001 " pdb=" C5' 2BA A1001 " pdb=" O4' 2BA A1001 " both_signs ideal model delta sigma weight residual False -2.39 -2.70 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA TYR B 81 " pdb=" N TYR B 81 " pdb=" C TYR B 81 " pdb=" CB TYR B 81 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 1451 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 280 " 0.040 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO B 281 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 281 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 281 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 280 " -0.040 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO A 281 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 88 " -0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO B 89 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 89 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 89 " -0.032 5.00e-02 4.00e+02 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 135 2.68 - 3.24: 9151 3.24 - 3.79: 14448 3.79 - 4.35: 18683 4.35 - 4.90: 30506 Nonbonded interactions: 72923 Sorted by model distance: nonbonded pdb=" OG1 THR B 277 " pdb=" OE1 GLN B 288 " model vdw 2.129 3.040 nonbonded pdb=" OG1 THR A 277 " pdb=" OE1 GLN A 288 " model vdw 2.129 3.040 nonbonded pdb=" OG SER A 127 " pdb=" O GLY A 368 " model vdw 2.318 3.040 nonbonded pdb=" OG SER B 127 " pdb=" O GLY B 368 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR A 284 " pdb=" OG SER A 287 " model vdw 2.328 3.040 ... (remaining 72918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.440 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.005 0.074 8910 Z= 0.351 Angle : 0.708 8.529 12130 Z= 0.353 Chirality : 0.045 0.310 1454 Planarity : 0.005 0.062 1458 Dihedral : 17.410 173.263 3240 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.27), residues: 1092 helix: 1.16 (0.20), residues: 768 sheet: -0.30 (0.60), residues: 84 loop : -1.59 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 404 HIS 0.002 0.001 HIS A 141 PHE 0.015 0.001 PHE B 319 TYR 0.013 0.001 TYR A 43 ARG 0.002 0.000 ARG B 589 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.867 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1905 time to fit residues: 42.2111 Evaluate side-chains 128 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 HIS B 372 HIS ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8910 Z= 0.222 Angle : 0.595 7.443 12130 Z= 0.302 Chirality : 0.041 0.161 1454 Planarity : 0.005 0.054 1458 Dihedral : 16.498 179.962 1296 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.43 % Allowed : 10.56 % Favored : 89.01 % 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: 1.26 (0.27), residues: 1092 helix: 1.59 (0.19), residues: 766 sheet: -0.07 (0.60), residues: 84 loop : -1.19 (0.44), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 404 HIS 0.002 0.001 HIS A 141 PHE 0.012 0.001 PHE A 242 TYR 0.014 0.001 TYR A 43 ARG 0.001 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.915 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 146 average time/residue: 0.1768 time to fit residues: 37.6614 Evaluate side-chains 130 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain B residue 84 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 8.9990 chunk 31 optimal weight: 0.3980 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 0.0030 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8910 Z= 0.206 Angle : 0.566 7.334 12130 Z= 0.286 Chirality : 0.040 0.150 1454 Planarity : 0.004 0.047 1458 Dihedral : 16.343 177.196 1296 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.08 % Allowed : 12.93 % Favored : 85.99 % 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: 1.41 (0.27), residues: 1092 helix: 1.70 (0.19), residues: 776 sheet: 0.04 (0.59), residues: 84 loop : -1.34 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 404 HIS 0.002 0.001 HIS A 141 PHE 0.023 0.001 PHE A 591 TYR 0.009 0.001 TYR A 536 ARG 0.001 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 1.086 Fit side-chains REVERT: A 547 LEU cc_start: 0.7977 (tp) cc_final: 0.7659 (tp) REVERT: B 547 LEU cc_start: 0.7973 (tp) cc_final: 0.7640 (tp) outliers start: 10 outliers final: 4 residues processed: 148 average time/residue: 0.1804 time to fit residues: 38.7392 Evaluate side-chains 136 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 588 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 11 optimal weight: 0.0870 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8910 Z= 0.205 Angle : 0.582 7.452 12130 Z= 0.291 Chirality : 0.040 0.135 1454 Planarity : 0.004 0.045 1458 Dihedral : 16.203 175.939 1296 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.51 % Allowed : 17.13 % Favored : 81.36 % 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: 1.37 (0.26), residues: 1092 helix: 1.69 (0.19), residues: 776 sheet: 0.17 (0.59), residues: 84 loop : -1.46 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 404 HIS 0.002 0.000 HIS A 141 PHE 0.019 0.001 PHE A 591 TYR 0.009 0.001 TYR B 43 ARG 0.001 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.986 Fit side-chains REVERT: A 397 ILE cc_start: 0.7628 (pt) cc_final: 0.7388 (mt) REVERT: A 477 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8247 (mt) REVERT: B 257 MET cc_start: 0.7807 (tmm) cc_final: 0.7597 (ttp) outliers start: 14 outliers final: 8 residues processed: 153 average time/residue: 0.1857 time to fit residues: 41.5405 Evaluate side-chains 136 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 588 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8910 Z= 0.261 Angle : 0.588 6.947 12130 Z= 0.294 Chirality : 0.041 0.151 1454 Planarity : 0.004 0.043 1458 Dihedral : 16.191 179.534 1296 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.48 % Allowed : 18.64 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.27), residues: 1092 helix: 1.68 (0.19), residues: 774 sheet: 0.15 (0.58), residues: 84 loop : -1.42 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 404 HIS 0.002 0.001 HIS B 141 PHE 0.030 0.001 PHE A 591 TYR 0.010 0.001 TYR B 95 ARG 0.001 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.898 Fit side-chains REVERT: A 440 MET cc_start: 0.8633 (mmp) cc_final: 0.8413 (mmp) REVERT: A 477 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8289 (mt) REVERT: B 440 MET cc_start: 0.8615 (mmp) cc_final: 0.8398 (mmp) outliers start: 23 outliers final: 7 residues processed: 157 average time/residue: 0.1666 time to fit residues: 38.5694 Evaluate side-chains 142 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 588 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8910 Z= 0.229 Angle : 0.577 6.884 12130 Z= 0.292 Chirality : 0.040 0.183 1454 Planarity : 0.004 0.044 1458 Dihedral : 15.983 179.573 1296 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.62 % Allowed : 19.61 % Favored : 78.77 % 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: 1.35 (0.27), residues: 1092 helix: 1.70 (0.19), residues: 772 sheet: 0.18 (0.58), residues: 84 loop : -1.54 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 404 HIS 0.007 0.001 HIS B 453 PHE 0.017 0.001 PHE A 591 TYR 0.007 0.001 TYR A 536 ARG 0.001 0.000 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.831 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 155 average time/residue: 0.1983 time to fit residues: 43.5873 Evaluate side-chains 143 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 588 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8910 Z= 0.209 Angle : 0.574 6.922 12130 Z= 0.288 Chirality : 0.039 0.137 1454 Planarity : 0.004 0.043 1458 Dihedral : 15.759 176.480 1296 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.51 % Allowed : 20.91 % Favored : 77.59 % 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: 1.38 (0.26), residues: 1092 helix: 1.74 (0.19), residues: 772 sheet: 0.25 (0.58), residues: 84 loop : -1.59 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 404 HIS 0.009 0.001 HIS B 453 PHE 0.010 0.001 PHE A 591 TYR 0.007 0.001 TYR A 536 ARG 0.001 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 1.014 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 151 average time/residue: 0.1876 time to fit residues: 40.8963 Evaluate side-chains 140 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 588 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8910 Z= 0.236 Angle : 0.620 9.866 12130 Z= 0.308 Chirality : 0.041 0.159 1454 Planarity : 0.004 0.045 1458 Dihedral : 15.781 177.371 1296 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.05 % Allowed : 20.91 % Favored : 77.05 % 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: 1.37 (0.26), residues: 1092 helix: 1.72 (0.19), residues: 772 sheet: 0.24 (0.58), residues: 84 loop : -1.55 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 404 HIS 0.010 0.001 HIS A 453 PHE 0.009 0.001 PHE A 242 TYR 0.008 0.001 TYR B 95 ARG 0.002 0.000 ARG B 528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.992 Fit side-chains REVERT: A 514 LYS cc_start: 0.8448 (tptm) cc_final: 0.8173 (tptp) REVERT: A 547 LEU cc_start: 0.7918 (tp) cc_final: 0.7525 (mp) REVERT: B 547 LEU cc_start: 0.7980 (tp) cc_final: 0.7570 (mp) outliers start: 19 outliers final: 14 residues processed: 149 average time/residue: 0.1787 time to fit residues: 38.6600 Evaluate side-chains 142 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 588 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 0.0470 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8910 Z= 0.219 Angle : 0.613 10.215 12130 Z= 0.301 Chirality : 0.040 0.143 1454 Planarity : 0.004 0.044 1458 Dihedral : 15.818 176.561 1296 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.94 % Allowed : 21.01 % Favored : 77.05 % 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: 1.40 (0.26), residues: 1092 helix: 1.73 (0.19), residues: 772 sheet: 0.24 (0.58), residues: 84 loop : -1.52 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 404 HIS 0.009 0.001 HIS A 453 PHE 0.009 0.001 PHE A 242 TYR 0.007 0.001 TYR B 95 ARG 0.001 0.000 ARG A 519 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.912 Fit side-chains REVERT: A 514 LYS cc_start: 0.8436 (tptm) cc_final: 0.8161 (tptp) REVERT: A 547 LEU cc_start: 0.7947 (tp) cc_final: 0.7550 (mp) REVERT: B 547 LEU cc_start: 0.7912 (tp) cc_final: 0.7548 (mp) outliers start: 18 outliers final: 15 residues processed: 150 average time/residue: 0.1782 time to fit residues: 39.0462 Evaluate side-chains 145 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 588 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 0.0470 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8910 Z= 0.216 Angle : 0.626 10.246 12130 Z= 0.309 Chirality : 0.041 0.169 1454 Planarity : 0.004 0.045 1458 Dihedral : 15.849 175.304 1296 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.72 % Allowed : 22.09 % Favored : 76.19 % 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: 1.44 (0.26), residues: 1092 helix: 1.73 (0.19), residues: 776 sheet: 0.31 (0.58), residues: 84 loop : -1.44 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 404 HIS 0.008 0.001 HIS A 453 PHE 0.009 0.001 PHE A 242 TYR 0.007 0.001 TYR A 536 ARG 0.001 0.000 ARG A 519 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.926 Fit side-chains REVERT: A 514 LYS cc_start: 0.8429 (tptm) cc_final: 0.8143 (tptp) REVERT: A 547 LEU cc_start: 0.7863 (tp) cc_final: 0.7547 (mp) REVERT: B 547 LEU cc_start: 0.7892 (tp) cc_final: 0.7567 (mp) outliers start: 16 outliers final: 15 residues processed: 145 average time/residue: 0.1901 time to fit residues: 40.0286 Evaluate side-chains 145 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 588 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN ** B 575 HIS ** 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 = 0.3744 r_free = 0.3744 target = 0.161631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.149967 restraints weight = 9706.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.149967 restraints weight = 9164.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.149967 restraints weight = 9164.769| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8910 Z= 0.223 Angle : 0.614 10.199 12130 Z= 0.299 Chirality : 0.040 0.154 1454 Planarity : 0.004 0.044 1458 Dihedral : 15.957 175.583 1296 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.94 % Allowed : 21.55 % Favored : 76.51 % 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: 1.42 (0.26), residues: 1092 helix: 1.73 (0.19), residues: 772 sheet: 0.30 (0.58), residues: 84 loop : -1.46 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 404 HIS 0.007 0.001 HIS B 453 PHE 0.009 0.001 PHE B 242 TYR 0.007 0.001 TYR B 95 ARG 0.001 0.000 ARG B 528 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1842.02 seconds wall clock time: 34 minutes 59.78 seconds (2099.78 seconds total)