Starting phenix.real_space_refine on Wed Jun 4 15:19:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3e_41859/06_2025/8u3e_41859.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3e_41859/06_2025/8u3e_41859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u3e_41859/06_2025/8u3e_41859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3e_41859/06_2025/8u3e_41859.map" model { file = "/net/cci-nas-00/data/ceres_data/8u3e_41859/06_2025/8u3e_41859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3e_41859/06_2025/8u3e_41859.cif" } resolution = 3.19 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= 0.004 sd= 0.073 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 2230 2.51 5 N 522 2.21 5 O 571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3338 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3338 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain breaks: 1 Time building chain proxies: 3.07, per 1000 atoms: 0.92 Number of scatterers: 3338 At special positions: 0 Unit cell: (62.25, 76.36, 81.34, 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 571 8.00 N 522 7.00 C 2230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 1.2 seconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 776 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 85.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 37 through 68 removed outlier: 3.502A pdb=" N PHE A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.621A pdb=" N GLN A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 124 through 134 removed outlier: 3.706A pdb=" N TYR A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 158 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 161 through 176 Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.787A pdb=" N ALA A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 224 removed outlier: 3.736A pdb=" N SER A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 226 through 247 removed outlier: 4.026A pdb=" N PHE A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 259 through 276 removed outlier: 4.886A pdb=" N ASN A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 319 removed outlier: 3.518A pdb=" N TRP A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 332 through 356 removed outlier: 4.178A pdb=" N GLY A 346 " --> pdb=" O MET A 342 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 360 removed outlier: 3.707A pdb=" N THR A 360 " --> pdb=" O ASN A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 361 through 385 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.509A pdb=" N GLY A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.919A pdb=" N ASP A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 removed outlier: 4.096A pdb=" N GLY A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 447 removed outlier: 3.577A pdb=" N MET A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 4.007A pdb=" N LYS A 445 " --> pdb=" O PRO A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 478 removed outlier: 4.113A pdb=" N THR A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) 233 hydrogen bonds defined for protein. 684 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: 0.86 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 982 1.34 - 1.46: 937 1.46 - 1.58: 1497 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3440 Sorted by residual: bond pdb=" N LEU A 45 " pdb=" CA LEU A 45 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.28e-02 6.10e+03 6.70e+00 bond pdb=" N THR A 107 " pdb=" CA THR A 107 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.17e+00 bond pdb=" N GLN A 123 " pdb=" CA GLN A 123 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.24e-02 6.50e+03 6.13e+00 bond pdb=" N ILE A 44 " pdb=" CA ILE A 44 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.37e-02 5.33e+03 5.86e+00 bond pdb=" CA VAL A 482 " pdb=" CB VAL A 482 " ideal model delta sigma weight residual 1.553 1.536 0.017 7.40e-03 1.83e+04 5.21e+00 ... (remaining 3435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 4382 1.26 - 2.52: 255 2.52 - 3.78: 45 3.78 - 5.04: 10 5.04 - 6.30: 2 Bond angle restraints: 4694 Sorted by residual: angle pdb=" N LEU A 45 " pdb=" CA LEU A 45 " pdb=" C LEU A 45 " ideal model delta sigma weight residual 113.88 107.58 6.30 1.23e+00 6.61e-01 2.63e+01 angle pdb=" N ILE A 44 " pdb=" CA ILE A 44 " pdb=" C ILE A 44 " ideal model delta sigma weight residual 112.83 107.84 4.99 9.90e-01 1.02e+00 2.55e+01 angle pdb=" N SER A 420 " pdb=" CA SER A 420 " pdb=" CB SER A 420 " ideal model delta sigma weight residual 114.17 110.82 3.35 1.14e+00 7.69e-01 8.64e+00 angle pdb=" C MET A 372 " pdb=" N ILE A 373 " pdb=" CA ILE A 373 " ideal model delta sigma weight residual 122.66 119.85 2.81 9.70e-01 1.06e+00 8.40e+00 angle pdb=" N ALA A 43 " pdb=" CA ALA A 43 " pdb=" C ALA A 43 " ideal model delta sigma weight residual 113.18 109.84 3.34 1.21e+00 6.83e-01 7.62e+00 ... (remaining 4689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.67: 1694 14.67 - 29.34: 192 29.34 - 44.01: 44 44.01 - 58.68: 4 58.68 - 73.35: 3 Dihedral angle restraints: 1937 sinusoidal: 716 harmonic: 1221 Sorted by residual: dihedral pdb=" CA GLN A 483 " pdb=" C GLN A 483 " pdb=" N ASN A 484 " pdb=" CA ASN A 484 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA TYR A 389 " pdb=" C TYR A 389 " pdb=" N SER A 390 " pdb=" CA SER A 390 " ideal model delta harmonic sigma weight residual -180.00 -163.80 -16.20 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA LEU A 476 " pdb=" C LEU A 476 " pdb=" N PHE A 477 " pdb=" CA PHE A 477 " ideal model delta harmonic sigma weight residual -180.00 -164.76 -15.24 0 5.00e+00 4.00e-02 9.30e+00 ... (remaining 1934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 271 0.032 - 0.064: 163 0.064 - 0.096: 79 0.096 - 0.128: 18 0.128 - 0.160: 2 Chirality restraints: 533 Sorted by residual: chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA PRO A 252 " pdb=" N PRO A 252 " pdb=" C PRO A 252 " pdb=" CB PRO A 252 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 530 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 289 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO A 290 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 214 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.22e+00 pdb=" N PRO A 215 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 124 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 125 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " 0.015 5.00e-02 4.00e+02 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1052 2.80 - 3.33: 3348 3.33 - 3.85: 5581 3.85 - 4.38: 6639 4.38 - 4.90: 11494 Nonbonded interactions: 28114 Sorted by model distance: nonbonded pdb=" OH TYR A 101 " pdb=" OD1 ASP A 158 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR A 40 " pdb=" OE2 GLU A 194 " model vdw 2.286 3.040 nonbonded pdb=" O SER A 213 " pdb=" OG SER A 217 " model vdw 2.371 3.040 nonbonded pdb=" O THR A 397 " pdb=" OG1 THR A 401 " model vdw 2.379 3.040 nonbonded pdb=" O THR A 448 " pdb=" OG1 THR A 448 " model vdw 2.380 3.040 ... (remaining 28109 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: 1.850 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.150 Find NCS groups from input model: 0.030 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:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 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 : 0.009 0.048 3440 Z= 0.358 Angle : 0.694 6.305 4694 Z= 0.416 Chirality : 0.047 0.160 533 Planarity : 0.004 0.033 569 Dihedral : 13.042 73.345 1161 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.34), residues: 423 helix: -1.91 (0.24), residues: 330 sheet: None (None), residues: 0 loop : -3.21 (0.51), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 244 HIS 0.004 0.001 HIS A 414 PHE 0.016 0.001 PHE A 232 TYR 0.014 0.001 TYR A 261 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.10740 ( 233) hydrogen bonds : angle 5.71434 ( 684) covalent geometry : bond 0.00896 ( 3440) covalent geometry : angle 0.69435 ( 4694) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.323 Fit side-chains REVERT: A 66 ASP cc_start: 0.7642 (t70) cc_final: 0.7035 (t0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1143 time to fit residues: 3.3011 Evaluate side-chains 18 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0040 chunk 31 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.143051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122311 restraints weight = 3851.458| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.79 r_work: 0.3285 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3440 Z= 0.137 Angle : 0.560 5.445 4694 Z= 0.293 Chirality : 0.043 0.150 533 Planarity : 0.005 0.043 569 Dihedral : 4.401 14.825 455 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.57 % Allowed : 9.38 % Favored : 90.06 % 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: -0.81 (0.41), residues: 423 helix: 0.02 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -2.27 (0.62), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 103 HIS 0.002 0.000 HIS A 414 PHE 0.017 0.001 PHE A 232 TYR 0.011 0.001 TYR A 335 ARG 0.001 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 233) hydrogen bonds : angle 4.57819 ( 684) covalent geometry : bond 0.00327 ( 3440) covalent geometry : angle 0.56011 ( 4694) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.348 Fit side-chains REVERT: A 66 ASP cc_start: 0.7970 (t70) cc_final: 0.7523 (t0) REVERT: A 249 SER cc_start: 0.9100 (t) cc_final: 0.8868 (t) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.1759 time to fit residues: 5.0842 Evaluate side-chains 21 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.139143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115340 restraints weight = 3970.266| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.94 r_work: 0.3261 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3440 Z= 0.150 Angle : 0.543 5.002 4694 Z= 0.285 Chirality : 0.044 0.144 533 Planarity : 0.005 0.044 569 Dihedral : 4.280 14.105 455 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.42 % Allowed : 11.08 % 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: -0.07 (0.42), residues: 423 helix: 0.52 (0.30), residues: 337 sheet: None (None), residues: 0 loop : -2.07 (0.64), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 103 HIS 0.003 0.001 HIS A 255 PHE 0.014 0.001 PHE A 232 TYR 0.013 0.001 TYR A 335 ARG 0.001 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 233) hydrogen bonds : angle 4.35831 ( 684) covalent geometry : bond 0.00366 ( 3440) covalent geometry : angle 0.54316 ( 4694) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.340 Fit side-chains REVERT: A 66 ASP cc_start: 0.8571 (t70) cc_final: 0.7932 (t0) REVERT: A 256 LYS cc_start: 0.8453 (mtmm) cc_final: 0.7685 (mtmm) outliers start: 5 outliers final: 2 residues processed: 28 average time/residue: 0.1637 time to fit residues: 5.9601 Evaluate side-chains 25 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.0070 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115550 restraints weight = 4110.889| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.99 r_work: 0.3257 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3440 Z= 0.125 Angle : 0.523 5.027 4694 Z= 0.272 Chirality : 0.041 0.140 533 Planarity : 0.005 0.045 569 Dihedral : 4.172 13.238 455 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.70 % Allowed : 12.78 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.43), residues: 423 helix: 0.86 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -1.68 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 356 HIS 0.001 0.000 HIS A 414 PHE 0.010 0.001 PHE A 232 TYR 0.010 0.001 TYR A 335 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 233) hydrogen bonds : angle 4.25503 ( 684) covalent geometry : bond 0.00295 ( 3440) covalent geometry : angle 0.52342 ( 4694) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.351 Fit side-chains REVERT: A 66 ASP cc_start: 0.8604 (t70) cc_final: 0.7993 (t0) REVERT: A 185 MET cc_start: 0.8823 (mtp) cc_final: 0.8585 (mtp) REVERT: A 256 LYS cc_start: 0.8435 (mtmm) cc_final: 0.7648 (mtmm) outliers start: 6 outliers final: 2 residues processed: 26 average time/residue: 0.1544 time to fit residues: 5.2420 Evaluate side-chains 25 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.137550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112998 restraints weight = 4110.589| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.00 r_work: 0.3241 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3440 Z= 0.135 Angle : 0.527 5.095 4694 Z= 0.275 Chirality : 0.042 0.141 533 Planarity : 0.005 0.046 569 Dihedral : 4.185 14.004 455 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.14 % Allowed : 14.49 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.43), residues: 423 helix: 0.97 (0.30), residues: 332 sheet: None (None), residues: 0 loop : -1.50 (0.63), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 356 HIS 0.001 0.000 HIS A 255 PHE 0.011 0.001 PHE A 299 TYR 0.011 0.001 TYR A 335 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 233) hydrogen bonds : angle 4.21938 ( 684) covalent geometry : bond 0.00327 ( 3440) covalent geometry : angle 0.52726 ( 4694) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.339 Fit side-chains REVERT: A 66 ASP cc_start: 0.8732 (t70) cc_final: 0.8113 (t0) REVERT: A 185 MET cc_start: 0.8886 (mtp) cc_final: 0.8661 (mtp) REVERT: A 256 LYS cc_start: 0.8487 (mtmm) cc_final: 0.7778 (mtmm) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.1548 time to fit residues: 4.9173 Evaluate side-chains 25 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.113420 restraints weight = 4217.159| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.02 r_work: 0.3235 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3440 Z= 0.132 Angle : 0.521 5.108 4694 Z= 0.271 Chirality : 0.042 0.138 533 Planarity : 0.005 0.046 569 Dihedral : 4.139 13.530 455 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.99 % Allowed : 14.77 % Favored : 83.24 % 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: 0.69 (0.43), residues: 423 helix: 1.08 (0.30), residues: 333 sheet: None (None), residues: 0 loop : -1.80 (0.61), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 103 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE A 299 TYR 0.011 0.001 TYR A 335 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 233) hydrogen bonds : angle 4.19021 ( 684) covalent geometry : bond 0.00320 ( 3440) covalent geometry : angle 0.52105 ( 4694) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.320 Fit side-chains REVERT: A 66 ASP cc_start: 0.8754 (t70) cc_final: 0.8129 (t0) REVERT: A 256 LYS cc_start: 0.8492 (mtmm) cc_final: 0.7777 (mtmm) REVERT: A 321 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7793 (mmm-85) outliers start: 7 outliers final: 4 residues processed: 30 average time/residue: 0.1866 time to fit residues: 6.9443 Evaluate side-chains 30 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.0000 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.138418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113875 restraints weight = 4143.648| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.00 r_work: 0.3254 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3440 Z= 0.118 Angle : 0.512 5.117 4694 Z= 0.266 Chirality : 0.041 0.137 533 Planarity : 0.005 0.046 569 Dihedral : 4.080 13.450 455 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.70 % Allowed : 15.62 % Favored : 82.67 % 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: 0.86 (0.42), residues: 423 helix: 1.19 (0.30), residues: 333 sheet: None (None), residues: 0 loop : -1.69 (0.61), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 103 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE A 299 TYR 0.009 0.001 TYR A 335 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 233) hydrogen bonds : angle 4.14936 ( 684) covalent geometry : bond 0.00276 ( 3440) covalent geometry : angle 0.51156 ( 4694) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.326 Fit side-chains REVERT: A 66 ASP cc_start: 0.8767 (t70) cc_final: 0.8139 (t0) REVERT: A 256 LYS cc_start: 0.8530 (mtmm) cc_final: 0.7845 (mtmm) REVERT: A 321 ARG cc_start: 0.8015 (mmm-85) cc_final: 0.7781 (mmm-85) outliers start: 6 outliers final: 5 residues processed: 29 average time/residue: 0.1912 time to fit residues: 6.9001 Evaluate side-chains 31 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 443 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.139118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.114843 restraints weight = 4177.256| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.01 r_work: 0.3252 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3440 Z= 0.118 Angle : 0.512 5.177 4694 Z= 0.265 Chirality : 0.041 0.137 533 Planarity : 0.005 0.046 569 Dihedral : 4.049 13.438 455 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.27 % Allowed : 15.06 % Favored : 82.67 % 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: 1.06 (0.43), residues: 423 helix: 1.27 (0.30), residues: 333 sheet: None (None), residues: 0 loop : -1.34 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 103 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE A 299 TYR 0.009 0.001 TYR A 335 ARG 0.001 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 233) hydrogen bonds : angle 4.10365 ( 684) covalent geometry : bond 0.00280 ( 3440) covalent geometry : angle 0.51162 ( 4694) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.316 Fit side-chains REVERT: A 66 ASP cc_start: 0.8764 (t70) cc_final: 0.8152 (t0) REVERT: A 256 LYS cc_start: 0.8552 (mtmm) cc_final: 0.7860 (mtmm) REVERT: A 321 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7817 (mmm-85) outliers start: 8 outliers final: 6 residues processed: 33 average time/residue: 0.1748 time to fit residues: 7.2208 Evaluate side-chains 33 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 443 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.139092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.114813 restraints weight = 4184.624| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.99 r_work: 0.3256 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3440 Z= 0.119 Angle : 0.519 5.528 4694 Z= 0.270 Chirality : 0.041 0.187 533 Planarity : 0.005 0.046 569 Dihedral : 4.028 13.379 455 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.70 % Allowed : 16.19 % Favored : 82.10 % 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: 1.14 (0.43), residues: 423 helix: 1.32 (0.30), residues: 333 sheet: None (None), residues: 0 loop : -1.26 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 103 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE A 299 TYR 0.009 0.001 TYR A 335 ARG 0.001 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 233) hydrogen bonds : angle 4.10460 ( 684) covalent geometry : bond 0.00282 ( 3440) covalent geometry : angle 0.51877 ( 4694) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.360 Fit side-chains REVERT: A 66 ASP cc_start: 0.8758 (t70) cc_final: 0.8131 (t0) REVERT: A 256 LYS cc_start: 0.8558 (mtmm) cc_final: 0.7863 (mtmm) REVERT: A 321 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7809 (mmm-85) outliers start: 6 outliers final: 6 residues processed: 29 average time/residue: 0.2020 time to fit residues: 7.3149 Evaluate side-chains 33 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 443 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 2 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.138382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113989 restraints weight = 4170.780| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.99 r_work: 0.3246 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3440 Z= 0.128 Angle : 0.525 5.393 4694 Z= 0.274 Chirality : 0.042 0.188 533 Planarity : 0.005 0.046 569 Dihedral : 4.055 13.416 455 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.99 % Allowed : 16.19 % Favored : 81.82 % 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: 1.12 (0.43), residues: 423 helix: 1.24 (0.30), residues: 338 sheet: None (None), residues: 0 loop : -1.13 (0.67), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 103 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE A 299 TYR 0.010 0.001 TYR A 335 ARG 0.001 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 233) hydrogen bonds : angle 4.12529 ( 684) covalent geometry : bond 0.00308 ( 3440) covalent geometry : angle 0.52543 ( 4694) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.356 Fit side-chains REVERT: A 175 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8329 (tt0) REVERT: A 256 LYS cc_start: 0.8567 (mtmm) cc_final: 0.7874 (mtmm) REVERT: A 321 ARG cc_start: 0.8061 (mmm-85) cc_final: 0.7827 (mmm-85) outliers start: 7 outliers final: 6 residues processed: 31 average time/residue: 0.2028 time to fit residues: 7.8782 Evaluate side-chains 34 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 443 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 22 optimal weight: 0.0870 chunk 3 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.139795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.115264 restraints weight = 4177.191| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.00 r_work: 0.3259 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3440 Z= 0.116 Angle : 0.516 5.952 4694 Z= 0.268 Chirality : 0.041 0.159 533 Planarity : 0.005 0.046 569 Dihedral : 4.014 13.340 455 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.42 % Allowed : 16.76 % Favored : 81.82 % 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: 1.21 (0.43), residues: 423 helix: 1.30 (0.30), residues: 339 sheet: None (None), residues: 0 loop : -1.10 (0.67), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 103 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE A 299 TYR 0.009 0.001 TYR A 335 ARG 0.001 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 233) hydrogen bonds : angle 4.08740 ( 684) covalent geometry : bond 0.00271 ( 3440) covalent geometry : angle 0.51567 ( 4694) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2054.97 seconds wall clock time: 36 minutes 8.82 seconds (2168.82 seconds total)