Starting phenix.real_space_refine on Thu Jul 18 21:05:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y66_38968/07_2024/8y66_38968.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y66_38968/07_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_38968/07_2024/8y66_38968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y66_38968/07_2024/8y66_38968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y66_38968/07_2024/8y66_38968.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y66_38968/07_2024/8y66_38968.cif" } 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-5388/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: 2.74, per 1000 atoms: 0.76 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: 1.41 Conformation dependent library (CDL) restraints added in 556.9 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... Secondary structure from input PDB file: 27 helices and 0 sheets defined 89.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 54 through 76 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) removed outlier: 3.594A pdb=" N SER A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 98 Processing helix chain 'A' and resid 102 through 136 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) removed outlier: 3.807A pdb=" N GLY A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 157 Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 163 through 182 removed outlier: 3.774A pdb=" N LEU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 197 through 220 Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.647A pdb=" N GLY A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 removed outlier: 4.454A pdb=" N VAL A 237 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 249 Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.930A pdb=" N GLU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 282 through 298 Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 313 through 330 Processing helix chain 'A' and resid 331 through 346 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 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 352 through 379 removed outlier: 4.010A pdb=" N LEU A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU A 376 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 404 removed outlier: 3.942A pdb=" N LEU A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 429 removed outlier: 3.570A pdb=" N LEU A 414 " --> pdb=" O TRP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 4.668A pdb=" N GLY A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 476 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 480 through 498 removed outlier: 4.527A pdb=" N PHE A 484 " --> pdb=" O CYS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 519 removed outlier: 3.652A pdb=" N ARG A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 831 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: 0.97 Time building geometry restraints manager: 1.54 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: 638 2.76 - 3.29: 3715 3.29 - 3.83: 6081 3.83 - 4.36: 6485 4.36 - 4.90: 11514 Nonbonded interactions: 28433 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 28428 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.170 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.450 ------------------------------------------------------------------------------- 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= 0.377 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 : 0.376 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: 0.1018 time to fit residues: 10.2917 Evaluate side-chains 63 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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: 0.7980 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.0020 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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: 0.6568 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3697 Z= 0.183 Angle : 0.568 5.407 5038 Z= 0.294 Chirality : 0.042 0.137 592 Planarity : 0.005 0.051 623 Dihedral : 4.185 14.293 507 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.34 % Allowed : 9.38 % Favored : 88.28 % 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: 1.36 (0.41), residues: 465 helix: 1.23 (0.28), residues: 384 sheet: None (None), residues: 0 loop : -0.36 (0.77), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 410 HIS 0.001 0.000 HIS A 139 PHE 0.022 0.002 PHE A 164 TYR 0.007 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 73 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.409 Fit side-chains REVERT: A 174 MET cc_start: 0.7118 (tpp) cc_final: 0.6869 (tpp) outliers start: 9 outliers final: 6 residues processed: 68 average time/residue: 0.1062 time to fit residues: 9.9557 Evaluate side-chains 65 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 489 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 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: 0.6584 moved from start: 0.1209 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= 0.202 Angle : 0.559 5.225 5038 Z= 0.288 Chirality : 0.042 0.138 592 Planarity : 0.004 0.039 623 Dihedral : 4.076 12.602 507 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.43 % Allowed : 11.72 % Favored : 83.85 % 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 (0.41), residues: 465 helix: 1.28 (0.28), residues: 385 sheet: None (None), residues: 0 loop : -0.41 (0.77), residues: 80 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 0.020 0.002 PHE A 514 TYR 0.011 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 76 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.338 Fit side-chains REVERT: A 102 ASP cc_start: 0.6142 (OUTLIER) cc_final: 0.5552 (p0) outliers start: 17 outliers final: 13 residues processed: 70 average time/residue: 0.0984 time to fit residues: 9.4802 Evaluate side-chains 70 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 125 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 208 PHE 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 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: 3.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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: 0.6613 moved from start: 0.1370 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= 0.217 Angle : 0.570 5.238 5038 Z= 0.293 Chirality : 0.044 0.157 592 Planarity : 0.004 0.038 623 Dihedral : 4.051 13.000 507 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 5.21 % Allowed : 13.54 % Favored : 81.25 % 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: 1.55 (0.42), residues: 465 helix: 1.38 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.33 (0.76), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.001 0.001 HIS A 139 PHE 0.017 0.002 PHE A 208 TYR 0.012 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: 20 poor density : 58 time to evaluate : 0.384 Fit side-chains REVERT: A 102 ASP cc_start: 0.6131 (OUTLIER) cc_final: 0.5809 (p0) outliers start: 20 outliers final: 17 residues processed: 72 average time/residue: 0.0984 time to fit residues: 9.7833 Evaluate side-chains 75 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 125 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 208 PHE 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 420 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: 0.5980 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 39 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.6581 moved from start: 0.1483 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= 0.175 Angle : 0.541 5.140 5038 Z= 0.279 Chirality : 0.042 0.146 592 Planarity : 0.004 0.036 623 Dihedral : 3.971 12.688 507 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: 1.74 (0.42), residues: 465 helix: 1.49 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.16 (0.77), residues: 86 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 0.015 0.001 PHE A 395 TYR 0.012 0.001 TYR A 188 ARG 0.001 0.000 ARG A 447 *********************** 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 74 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 57 time to evaluate : 0.401 Fit side-chains REVERT: A 102 ASP cc_start: 0.6086 (OUTLIER) cc_final: 0.5762 (p0) outliers start: 17 outliers final: 13 residues processed: 69 average time/residue: 0.0990 time to fit residues: 9.4965 Evaluate side-chains 71 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 205 THR Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 360 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 42 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.6571 moved from start: 0.1573 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= 0.173 Angle : 0.549 8.869 5038 Z= 0.280 Chirality : 0.042 0.150 592 Planarity : 0.004 0.035 623 Dihedral : 3.927 12.391 507 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.21 % Allowed : 15.89 % Favored : 78.91 % 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: 1.82 (0.42), residues: 465 helix: 1.54 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.06 (0.76), residues: 86 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 0.015 0.001 PHE A 208 TYR 0.013 0.001 TYR A 188 ARG 0.001 0.000 ARG A 447 *********************** 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 80 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 0.380 Fit side-chains REVERT: A 102 ASP cc_start: 0.6072 (OUTLIER) cc_final: 0.5751 (p0) REVERT: A 444 GLN cc_start: 0.7371 (tm-30) cc_final: 0.7149 (tm-30) outliers start: 20 outliers final: 14 residues processed: 76 average time/residue: 0.1082 time to fit residues: 11.1078 Evaluate side-chains 72 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 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 205 THR Chi-restraints excluded: chain A residue 208 PHE 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 414 LEU 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: 0.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.0970 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.6596 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3697 Z= 0.201 Angle : 0.566 6.968 5038 Z= 0.289 Chirality : 0.043 0.153 592 Planarity : 0.004 0.037 623 Dihedral : 3.951 12.377 507 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.21 % Allowed : 15.62 % Favored : 79.17 % 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: 1.76 (0.41), residues: 465 helix: 1.50 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -0.10 (0.76), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 231 HIS 0.001 0.001 HIS A 139 PHE 0.027 0.002 PHE A 164 TYR 0.012 0.001 TYR A 188 ARG 0.001 0.000 ARG A 447 *********************** 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 75 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 55 time to evaluate : 0.352 Fit side-chains REVERT: A 102 ASP cc_start: 0.6043 (OUTLIER) cc_final: 0.5691 (p0) outliers start: 20 outliers final: 14 residues processed: 73 average time/residue: 0.1107 time to fit residues: 10.8486 Evaluate side-chains 68 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 53 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 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 205 THR Chi-restraints excluded: chain A residue 208 PHE 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 506 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 21 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 0.0070 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** 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: 0.6562 moved from start: 0.1743 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= 0.172 Angle : 0.571 7.978 5038 Z= 0.290 Chirality : 0.042 0.156 592 Planarity : 0.004 0.034 623 Dihedral : 3.948 12.119 507 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.43 % Allowed : 16.67 % Favored : 78.91 % 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: 1.90 (0.42), residues: 465 helix: 1.58 (0.28), residues: 379 sheet: None (None), residues: 0 loop : 0.04 (0.77), residues: 86 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 0.019 0.001 TYR A 188 ARG 0.010 0.000 ARG A 505 *********************** 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 72 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.370 Fit side-chains REVERT: A 102 ASP cc_start: 0.5990 (OUTLIER) cc_final: 0.5657 (p0) outliers start: 17 outliers final: 12 residues processed: 69 average time/residue: 0.0962 time to fit residues: 9.2480 Evaluate side-chains 66 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 116 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 205 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 427 CYS 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: 0.0470 chunk 12 optimal weight: 0.0370 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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 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: 0.6545 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3697 Z= 0.175 Angle : 0.597 8.769 5038 Z= 0.298 Chirality : 0.045 0.373 592 Planarity : 0.004 0.033 623 Dihedral : 3.938 11.947 507 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.39 % Allowed : 17.71 % Favored : 78.91 % 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: 1.83 (0.41), residues: 465 helix: 1.56 (0.28), residues: 380 sheet: None (None), residues: 0 loop : -0.18 (0.76), 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 139 PHE 0.023 0.001 PHE A 164 TYR 0.008 0.001 TYR A 73 ARG 0.008 0.000 ARG A 505 *********************** 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 66 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.375 Fit side-chains REVERT: A 102 ASP cc_start: 0.5971 (OUTLIER) cc_final: 0.5641 (p0) outliers start: 13 outliers final: 11 residues processed: 66 average time/residue: 0.1022 time to fit residues: 9.2965 Evaluate side-chains 62 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 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 205 THR Chi-restraints excluded: chain A residue 360 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 427 CYS 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: 1.9990 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 0.0070 chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 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: 0.6553 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3697 Z= 0.185 Angle : 0.587 7.383 5038 Z= 0.297 Chirality : 0.044 0.308 592 Planarity : 0.004 0.034 623 Dihedral : 3.934 11.718 507 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.39 % Allowed : 17.45 % Favored : 79.17 % 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: 1.87 (0.41), residues: 465 helix: 1.60 (0.28), residues: 380 sheet: None (None), residues: 0 loop : -0.22 (0.75), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.024 0.001 PHE A 164 TYR 0.008 0.001 TYR A 327 ARG 0.007 0.000 ARG A 505 ********************** 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 65 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.350 Fit side-chains REVERT: A 102 ASP cc_start: 0.5982 (OUTLIER) cc_final: 0.5628 (p0) REVERT: A 174 MET cc_start: 0.7769 (mmm) cc_final: 0.7476 (mmm) outliers start: 13 outliers final: 10 residues processed: 64 average time/residue: 0.1036 time to fit residues: 9.1495 Evaluate side-chains 62 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 116 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 360 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 427 CYS 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: 0.5980 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.0030 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 333 ASN A 462 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.225982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.188252 restraints weight = 4404.096| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 3.10 r_work: 0.4120 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3697 Z= 0.177 Angle : 0.580 7.558 5038 Z= 0.293 Chirality : 0.043 0.263 592 Planarity : 0.004 0.034 623 Dihedral : 3.899 11.593 507 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.17 % Allowed : 16.67 % Favored : 79.17 % 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: 1.91 (0.41), residues: 465 helix: 1.64 (0.28), residues: 380 sheet: None (None), residues: 0 loop : -0.25 (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 139 PHE 0.024 0.001 PHE A 164 TYR 0.008 0.001 TYR A 327 ARG 0.007 0.000 ARG A 505 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1082.05 seconds wall clock time: 19 minutes 55.22 seconds (1195.22 seconds total)