Starting phenix.real_space_refine on Mon Jun 24 17:11:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y66_38968/06_2024/8y66_38968_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y66_38968/06_2024/8y66_38968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y66_38968/06_2024/8y66_38968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y66_38968/06_2024/8y66_38968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y66_38968/06_2024/8y66_38968_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y66_38968/06_2024/8y66_38968_updated.pdb" } resolution = 3.28 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= 0.008 sd= 0.100 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 15 5.16 5 C 2385 2.51 5 N 580 2.21 5 O 626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3606 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3586 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'AGI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.87, per 1000 atoms: 0.80 Number of scatterers: 3606 At special positions: 0 Unit cell: (83.3525, 63.8675, 70.3625, 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 15 16.00 O 626 8.00 N 580 7.00 C 2385 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 - 3.50 Amino acid : False - 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: 1.56 Conformation dependent library (CDL) restraints added in 611.5 milliseconds 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 0 sheets defined 80.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 55 through 75 removed outlier: 4.222A pdb=" N PHE A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 97 Processing helix chain 'A' and resid 103 through 135 removed outlier: 4.716A pdb=" N PHE A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ALA A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LYS A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 161 removed outlier: 3.681A pdb=" N SER A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLN A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 181 Processing helix chain 'A' and resid 185 through 191 Processing helix chain 'A' and resid 195 through 219 removed outlier: 3.616A pdb=" N ARG A 198 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLY A 199 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 No H-bonds generated for 'chain 'A' and resid 222 through 225' Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 237 through 251 Proline residue: A 241 - end of helix removed outlier: 4.636A pdb=" N LEU A 249 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 283 through 297 Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 311 through 329 removed outlier: 3.534A pdb=" N ARG A 314 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N TRP A 315 " --> pdb=" O TYR A 312 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 328 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 329 " --> pdb=" O CYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 345 removed outlier: 6.386A pdb=" N ASN A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 378 removed outlier: 3.646A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Proline residue: A 354 - end of helix removed outlier: 5.147A pdb=" N ILE A 375 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 378 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 403 Processing helix chain 'A' and resid 409 through 428 Proline residue: A 412 - end of helix removed outlier: 3.908A pdb=" N SER A 428 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 441 removed outlier: 4.261A pdb=" N LEU A 437 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N THR A 438 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 441 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 475 removed outlier: 3.546A pdb=" N GLY A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 481 through 497 Processing helix chain 'A' and resid 507 through 518 removed outlier: 3.652A pdb=" N ARG A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 516 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: 0.95 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 548 1.31 - 1.44: 1011 1.44 - 1.56: 2116 1.56 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 3697 Sorted by residual: bond pdb=" CAS AGI A 601 " pdb=" OAL AGI A 601 " ideal model delta sigma weight residual 1.350 1.494 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" CAJ AGI A 601 " pdb=" CAQ AGI A 601 " ideal model delta sigma weight residual 1.354 1.485 -0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" CAO AGI A 601 " pdb=" OAD AGI A 601 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" CAQ AGI A 601 " pdb=" OAL AGI A 601 " ideal model delta sigma weight residual 1.341 1.461 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" CAM AGI A 601 " pdb=" OAB AGI A 601 " ideal model delta sigma weight residual 1.339 1.449 -0.110 2.00e-02 2.50e+03 3.00e+01 ... (remaining 3692 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.43: 85 105.43 - 112.58: 1921 112.58 - 119.72: 1246 119.72 - 126.87: 1737 126.87 - 134.01: 49 Bond angle restraints: 5038 Sorted by residual: angle pdb=" CA PHE A 235 " pdb=" CB PHE A 235 " pdb=" CG PHE A 235 " ideal model delta sigma weight residual 113.80 121.43 -7.63 1.00e+00 1.00e+00 5.83e+01 angle pdb=" N PHE A 235 " pdb=" CA PHE A 235 " pdb=" C PHE A 235 " ideal model delta sigma weight residual 112.59 104.30 8.29 1.22e+00 6.72e-01 4.61e+01 angle pdb=" C LEU A 234 " pdb=" N PHE A 235 " pdb=" CA PHE A 235 " ideal model delta sigma weight residual 122.67 112.31 10.36 1.59e+00 3.96e-01 4.24e+01 angle pdb=" N LEU A 234 " pdb=" CA LEU A 234 " pdb=" C LEU A 234 " ideal model delta sigma weight residual 112.90 104.60 8.30 1.31e+00 5.83e-01 4.02e+01 angle pdb=" C PHE A 235 " pdb=" CA PHE A 235 " pdb=" CB PHE A 235 " ideal model delta sigma weight residual 111.02 118.18 -7.16 1.61e+00 3.86e-01 1.98e+01 ... (remaining 5033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 1924 17.77 - 35.54: 191 35.54 - 53.31: 26 53.31 - 71.07: 4 71.07 - 88.84: 3 Dihedral angle restraints: 2148 sinusoidal: 818 harmonic: 1330 Sorted by residual: dihedral pdb=" CA ASP A 102 " pdb=" C ASP A 102 " pdb=" N PRO A 103 " pdb=" CA PRO A 103 " ideal model delta harmonic sigma weight residual -180.00 -161.12 -18.88 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CB GLU A 292 " pdb=" CG GLU A 292 " pdb=" CD GLU A 292 " pdb=" OE1 GLU A 292 " ideal model delta sinusoidal sigma weight residual 0.00 -88.84 88.84 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CG ARG A 447 " pdb=" CD ARG A 447 " pdb=" NE ARG A 447 " pdb=" CZ ARG A 447 " ideal model delta sinusoidal sigma weight residual -90.00 -132.68 42.68 2 1.50e+01 4.44e-03 9.80e+00 ... (remaining 2145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 397 0.041 - 0.082: 153 0.082 - 0.123: 32 0.123 - 0.164: 9 0.164 - 0.206: 1 Chirality restraints: 592 Sorted by residual: chirality pdb=" CA PHE A 235 " pdb=" N PHE A 235 " pdb=" C PHE A 235 " pdb=" CB PHE A 235 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE A 197 " pdb=" CA ILE A 197 " pdb=" CG1 ILE A 197 " pdb=" CG2 ILE A 197 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CB ILE A 335 " pdb=" CA ILE A 335 " pdb=" CG1 ILE A 335 " pdb=" CG2 ILE A 335 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 589 not shown) Planarity restraints: 623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 233 " 0.026 2.00e-02 2.50e+03 5.48e-02 3.01e+01 pdb=" C TYR A 233 " -0.095 2.00e-02 2.50e+03 pdb=" O TYR A 233 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU A 234 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 469 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PRO A 470 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 470 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 470 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 235 " 0.023 2.00e-02 2.50e+03 1.83e-02 5.83e+00 pdb=" CG PHE A 235 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 235 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 235 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 235 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 235 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 235 " 0.006 2.00e-02 2.50e+03 ... (remaining 620 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 637 2.76 - 3.29: 3773 3.29 - 3.83: 6079 3.83 - 4.36: 6558 4.36 - 4.90: 11526 Nonbonded interactions: 28573 Sorted by model distance: nonbonded pdb=" OE1 GLU A 191 " pdb=" OG SER A 255 " model vdw 2.223 2.440 nonbonded pdb=" O VAL A 356 " pdb=" OG SER A 359 " model vdw 2.269 2.440 nonbonded pdb=" O GLY A 136 " pdb=" OG1 THR A 140 " model vdw 2.278 2.440 nonbonded pdb=" OE2 GLU A 501 " pdb=" NH1 ARG A 505 " model vdw 2.381 2.520 nonbonded pdb=" O GLU A 223 " pdb=" NZ LYS A 227 " model vdw 2.388 2.520 ... (remaining 28568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 0.300 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: 1.590 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.480 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 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 : 0.006 0.144 3697 Z= 0.412 Angle : 0.765 10.358 5038 Z= 0.436 Chirality : 0.045 0.206 592 Planarity : 0.006 0.075 623 Dihedral : 14.110 88.841 1300 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.26 % Allowed : 1.04 % Favored : 98.70 % 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: 1.27 (0.41), residues: 465 helix: 1.14 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.19 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 231 HIS 0.002 0.001 HIS A 139 PHE 0.042 0.002 PHE A 235 TYR 0.011 0.001 TYR A 327 ARG 0.002 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.456 Fit side-chains REVERT: A 102 ASP cc_start: 0.6624 (p0) cc_final: 0.6207 (p0) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.1058 time to fit residues: 10.6484 Evaluate side-chains 63 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3697 Z= 0.201 Angle : 0.579 5.505 5038 Z= 0.318 Chirality : 0.043 0.147 592 Planarity : 0.007 0.048 623 Dihedral : 4.182 17.879 507 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.12 % Allowed : 9.38 % Favored : 87.50 % 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: 0.64 (0.40), residues: 465 helix: 0.66 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.16 (0.74), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 377 PHE 0.023 0.002 PHE A 164 TYR 0.011 0.001 TYR A 327 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.556 Fit side-chains REVERT: A 102 ASP cc_start: 0.6648 (p0) cc_final: 0.6095 (p0) REVERT: A 174 MET cc_start: 0.7412 (tpp) cc_final: 0.7184 (tpp) REVERT: A 203 GLN cc_start: 0.7910 (mm-40) cc_final: 0.6522 (tt0) outliers start: 12 outliers final: 10 residues processed: 74 average time/residue: 0.1005 time to fit residues: 10.2392 Evaluate side-chains 77 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3697 Z= 0.221 Angle : 0.567 5.450 5038 Z= 0.305 Chirality : 0.043 0.139 592 Planarity : 0.006 0.039 623 Dihedral : 4.072 18.327 507 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.43 % Allowed : 13.28 % Favored : 82.29 % 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: 0.48 (0.40), residues: 465 helix: 0.54 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -0.14 (0.71), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.018 0.002 PHE A 208 TYR 0.010 0.001 TYR A 188 ARG 0.001 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 0.404 Fit side-chains REVERT: A 203 GLN cc_start: 0.8136 (mm-40) cc_final: 0.6757 (tt0) outliers start: 17 outliers final: 13 residues processed: 75 average time/residue: 0.1001 time to fit residues: 10.3398 Evaluate side-chains 77 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3697 Z= 0.189 Angle : 0.556 9.352 5038 Z= 0.293 Chirality : 0.042 0.135 592 Planarity : 0.005 0.038 623 Dihedral : 3.999 17.462 507 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.43 % Allowed : 15.10 % Favored : 80.47 % 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: 0.53 (0.41), residues: 465 helix: 0.56 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -0.01 (0.70), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.015 0.001 PHE A 208 TYR 0.010 0.001 TYR A 188 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.369 Fit side-chains REVERT: A 102 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.6105 (p0) REVERT: A 316 GLN cc_start: 0.8338 (mt0) cc_final: 0.8128 (mt0) outliers start: 17 outliers final: 14 residues processed: 72 average time/residue: 0.0987 time to fit residues: 9.8972 Evaluate side-chains 76 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 0.0040 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3697 Z= 0.176 Angle : 0.533 5.189 5038 Z= 0.284 Chirality : 0.041 0.134 592 Planarity : 0.005 0.037 623 Dihedral : 3.908 16.592 507 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.69 % Allowed : 15.62 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.41), residues: 465 helix: 0.58 (0.28), residues: 375 sheet: None (None), residues: 0 loop : 0.04 (0.70), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.017 0.001 PHE A 208 TYR 0.011 0.001 TYR A 188 ARG 0.001 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 0.400 Fit side-chains REVERT: A 102 ASP cc_start: 0.6578 (OUTLIER) cc_final: 0.6038 (p0) REVERT: A 116 ILE cc_start: 0.5799 (OUTLIER) cc_final: 0.5523 (tp) REVERT: A 316 GLN cc_start: 0.8342 (mt0) cc_final: 0.8097 (mt0) REVERT: A 444 GLN cc_start: 0.7103 (tm-30) cc_final: 0.6873 (tm-30) outliers start: 18 outliers final: 14 residues processed: 72 average time/residue: 0.1037 time to fit residues: 10.3252 Evaluate side-chains 77 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 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 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3697 Z= 0.197 Angle : 0.545 5.244 5038 Z= 0.290 Chirality : 0.042 0.140 592 Planarity : 0.005 0.037 623 Dihedral : 3.890 16.360 507 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.47 % Allowed : 15.89 % Favored : 78.65 % 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: 0.51 (0.41), residues: 465 helix: 0.55 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -0.05 (0.69), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.018 0.002 PHE A 208 TYR 0.010 0.001 TYR A 188 ARG 0.002 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 62 time to evaluate : 0.425 Fit side-chains REVERT: A 102 ASP cc_start: 0.6617 (OUTLIER) cc_final: 0.6049 (p0) REVERT: A 116 ILE cc_start: 0.5733 (OUTLIER) cc_final: 0.5467 (tp) outliers start: 21 outliers final: 15 residues processed: 75 average time/residue: 0.1038 time to fit residues: 10.7119 Evaluate side-chains 78 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3697 Z= 0.186 Angle : 0.559 9.525 5038 Z= 0.292 Chirality : 0.041 0.138 592 Planarity : 0.005 0.037 623 Dihedral : 3.889 16.115 507 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.69 % Allowed : 17.19 % Favored : 78.12 % 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: 0.52 (0.41), residues: 465 helix: 0.53 (0.28), residues: 378 sheet: None (None), residues: 0 loop : 0.08 (0.72), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.028 0.002 PHE A 164 TYR 0.011 0.001 TYR A 188 ARG 0.001 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 58 time to evaluate : 0.406 Fit side-chains REVERT: A 102 ASP cc_start: 0.6539 (OUTLIER) cc_final: 0.5960 (p0) REVERT: A 116 ILE cc_start: 0.5803 (OUTLIER) cc_final: 0.5531 (tp) outliers start: 18 outliers final: 14 residues processed: 71 average time/residue: 0.1074 time to fit residues: 10.5895 Evaluate side-chains 75 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 chunk 21 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 245 GLN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3697 Z= 0.179 Angle : 0.549 8.467 5038 Z= 0.288 Chirality : 0.041 0.137 592 Planarity : 0.005 0.037 623 Dihedral : 3.863 15.905 507 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.95 % Allowed : 17.71 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.41), residues: 465 helix: 0.54 (0.28), residues: 378 sheet: None (None), residues: 0 loop : 0.17 (0.72), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.023 0.001 PHE A 164 TYR 0.011 0.001 TYR A 188 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 0.404 Fit side-chains REVERT: A 102 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.6006 (p0) REVERT: A 116 ILE cc_start: 0.5734 (OUTLIER) cc_final: 0.5466 (tp) outliers start: 19 outliers final: 15 residues processed: 75 average time/residue: 0.1009 time to fit residues: 10.2776 Evaluate side-chains 78 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3697 Z= 0.188 Angle : 0.562 8.695 5038 Z= 0.293 Chirality : 0.042 0.139 592 Planarity : 0.005 0.038 623 Dihedral : 3.869 15.906 507 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.43 % Allowed : 17.97 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.41), residues: 465 helix: 0.52 (0.28), residues: 377 sheet: None (None), residues: 0 loop : 0.19 (0.71), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.024 0.001 PHE A 164 TYR 0.011 0.001 TYR A 188 ARG 0.001 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 0.430 Fit side-chains REVERT: A 101 ILE cc_start: 0.4596 (OUTLIER) cc_final: 0.4024 (tt) REVERT: A 102 ASP cc_start: 0.6575 (OUTLIER) cc_final: 0.6170 (p0) outliers start: 17 outliers final: 14 residues processed: 73 average time/residue: 0.1023 time to fit residues: 10.2535 Evaluate side-chains 75 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 0.0170 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3697 Z= 0.174 Angle : 0.563 9.678 5038 Z= 0.292 Chirality : 0.041 0.136 592 Planarity : 0.005 0.037 623 Dihedral : 3.834 15.634 507 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.39 % Allowed : 19.79 % Favored : 76.82 % 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: 0.63 (0.41), residues: 465 helix: 0.56 (0.28), residues: 377 sheet: None (None), residues: 0 loop : 0.36 (0.72), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.022 0.001 PHE A 164 TYR 0.013 0.001 TYR A 188 ARG 0.001 0.000 ARG A 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.408 Fit side-chains REVERT: A 101 ILE cc_start: 0.4564 (OUTLIER) cc_final: 0.3975 (tt) REVERT: A 102 ASP cc_start: 0.6507 (OUTLIER) cc_final: 0.6103 (p0) REVERT: A 174 MET cc_start: 0.7713 (mmm) cc_final: 0.7387 (mmm) outliers start: 13 outliers final: 10 residues processed: 70 average time/residue: 0.0970 time to fit residues: 9.3880 Evaluate side-chains 71 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 506 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 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 = 0.4539 r_free = 0.4539 target = 0.219201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.182869 restraints weight = 4475.394| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 3.10 r_work: 0.4077 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3697 Z= 0.186 Angle : 0.575 9.271 5038 Z= 0.297 Chirality : 0.041 0.137 592 Planarity : 0.005 0.038 623 Dihedral : 3.868 15.727 507 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.39 % Allowed : 20.83 % Favored : 75.78 % 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: 0.61 (0.41), residues: 465 helix: 0.56 (0.28), residues: 377 sheet: None (None), residues: 0 loop : 0.26 (0.71), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.028 0.001 PHE A 164 TYR 0.007 0.001 TYR A 258 ARG 0.001 0.000 ARG A 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1112.80 seconds wall clock time: 21 minutes 2.66 seconds (1262.66 seconds total)