Starting phenix.real_space_refine on Tue Feb 11 00:12:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3e_41859/02_2025/8u3e_41859.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3e_41859/02_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_41859/02_2025/8u3e_41859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3e_41859/02_2025/8u3e_41859.map" model { file = "/net/cci-nas-00/data/ceres_data/8u3e_41859/02_2025/8u3e_41859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3e_41859/02_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-5592/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: 2.90, per 1000 atoms: 0.87 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: 0.79 Conformation dependent library (CDL) restraints added in 437.0 milliseconds 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: 0.94 Time building geometry restraints manager: 0.93 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.780 Find NCS groups from input model: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.080 ------------------------------------------------------------------------------- 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= 0.564 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 *********************** 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 : 0.363 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: 0.0977 time to fit residues: 2.8724 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 : 0.258 ------------------------------------------------------------------------------- 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: 0.3283 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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= 0.203 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 *********************** 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 : 0.353 Fit side-chains REVERT: A 66 ASP cc_start: 0.7972 (t70) cc_final: 0.7525 (t0) REVERT: A 249 SER cc_start: 0.9100 (t) cc_final: 0.8871 (t) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.1751 time to fit residues: 4.9802 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 : 0.355 ------------------------------------------------------------------------------- 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: 0.7980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.138505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113968 restraints weight = 3968.042| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.04 r_work: 0.3254 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3440 Z= 0.230 Angle : 0.550 4.945 4694 Z= 0.288 Chirality : 0.044 0.145 533 Planarity : 0.005 0.043 569 Dihedral : 4.285 14.173 455 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.42 % Allowed : 11.65 % Favored : 86.93 % 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: -0.09 (0.42), residues: 423 helix: 0.51 (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 0.013 0.001 PHE A 232 TYR 0.013 0.001 TYR A 335 ARG 0.001 0.000 ARG A 364 *********************** 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 : 0.360 Fit side-chains REVERT: A 66 ASP cc_start: 0.8567 (t70) cc_final: 0.7918 (t0) REVERT: A 256 LYS cc_start: 0.8438 (mtmm) cc_final: 0.7627 (mtmm) outliers start: 5 outliers final: 2 residues processed: 28 average time/residue: 0.1642 time to fit residues: 5.9030 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 : 0.321 ------------------------------------------------------------------------------- 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: 0.2980 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 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 = 0.3690 r_free = 0.3690 target = 0.138902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.114626 restraints weight = 4135.579| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.00 r_work: 0.3246 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2498 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= 0.203 Angle : 0.532 5.000 4694 Z= 0.277 Chirality : 0.042 0.141 533 Planarity : 0.005 0.045 569 Dihedral : 4.206 13.273 455 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.42 % Allowed : 13.35 % Favored : 85.23 % 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: 0.39 (0.42), residues: 423 helix: 0.83 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -1.67 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 356 HIS 0.001 0.000 HIS A 255 PHE 0.011 0.001 PHE A 299 TYR 0.010 0.001 TYR A 335 ARG 0.001 0.000 ARG A 364 *********************** 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: 5 poor density : 24 time to evaluate : 0.322 Fit side-chains REVERT: A 66 ASP cc_start: 0.8685 (t70) cc_final: 0.8053 (t0) REVERT: A 256 LYS cc_start: 0.8478 (mtmm) cc_final: 0.7710 (mtmm) outliers start: 5 outliers final: 2 residues processed: 27 average time/residue: 0.1617 time to fit residues: 5.7507 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 : 0.354 ------------------------------------------------------------------------------- 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: 0.6980 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 0.0770 chunk 13 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.137219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.112885 restraints weight = 4139.120| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.00 r_work: 0.3231 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3440 Z= 0.214 Angle : 0.531 5.072 4694 Z= 0.278 Chirality : 0.042 0.141 533 Planarity : 0.005 0.046 569 Dihedral : 4.224 13.805 455 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.70 % Allowed : 14.77 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.43), residues: 423 helix: 0.94 (0.30), residues: 334 sheet: None (None), residues: 0 loop : -1.44 (0.64), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 103 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 *********************** 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 30 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.318 Fit side-chains REVERT: A 66 ASP cc_start: 0.8736 (t70) cc_final: 0.8120 (t0) REVERT: A 256 LYS cc_start: 0.8497 (mtmm) cc_final: 0.7731 (mtmm) REVERT: A 321 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7807 (mmm-85) outliers start: 6 outliers final: 2 residues processed: 26 average time/residue: 0.1954 time to fit residues: 6.3447 Evaluate side-chains 26 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.136996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.112418 restraints weight = 4244.070| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.02 r_work: 0.3233 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2898 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= 0.197 Angle : 0.524 5.095 4694 Z= 0.272 Chirality : 0.041 0.139 533 Planarity : 0.005 0.046 569 Dihedral : 4.158 13.565 455 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.99 % Allowed : 15.34 % 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: 0.69 (0.43), residues: 423 helix: 1.09 (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 0.010 0.001 TYR A 335 ARG 0.001 0.000 ARG A 364 *********************** 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 : 0.266 Fit side-chains REVERT: A 66 ASP cc_start: 0.8745 (t70) cc_final: 0.8104 (t0) REVERT: A 256 LYS cc_start: 0.8536 (mtmm) cc_final: 0.7831 (mtmm) REVERT: A 321 ARG cc_start: 0.8057 (mmm-85) cc_final: 0.7821 (mmm-85) outliers start: 7 outliers final: 5 residues processed: 30 average time/residue: 0.1902 time to fit residues: 7.1316 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 : 0.329 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.138693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.114010 restraints weight = 4172.667| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.03 r_work: 0.3238 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3020 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= 0.185 Angle : 0.521 5.113 4694 Z= 0.270 Chirality : 0.041 0.137 533 Planarity : 0.005 0.046 569 Dihedral : 4.109 13.488 455 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.70 % Allowed : 15.91 % Favored : 82.39 % 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 (0.43), residues: 423 helix: 1.20 (0.30), residues: 333 sheet: None (None), residues: 0 loop : -1.72 (0.61), 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 0.010 0.001 TYR A 335 ARG 0.001 0.000 ARG A 57 *********************** 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 31 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.328 Fit side-chains REVERT: A 66 ASP cc_start: 0.8753 (t70) cc_final: 0.8123 (t0) REVERT: A 256 LYS cc_start: 0.8547 (mtmm) cc_final: 0.7851 (mtmm) REVERT: A 321 ARG cc_start: 0.8036 (mmm-85) cc_final: 0.7798 (mmm-85) outliers start: 6 outliers final: 5 residues processed: 28 average time/residue: 0.2071 time to fit residues: 7.2172 Evaluate side-chains 30 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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: 0.5980 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.1980 chunk 0 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.138851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114140 restraints weight = 4176.100| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.02 r_work: 0.3250 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3092 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= 0.164 Angle : 0.508 5.354 4694 Z= 0.263 Chirality : 0.041 0.137 533 Planarity : 0.005 0.046 569 Dihedral : 4.037 13.184 455 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.99 % Allowed : 15.62 % Favored : 82.39 % 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: 0.97 (0.43), residues: 423 helix: 1.28 (0.30), residues: 333 sheet: None (None), residues: 0 loop : -1.67 (0.62), 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 168 *********************** 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 35 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.387 Fit side-chains REVERT: A 66 ASP cc_start: 0.8757 (t70) cc_final: 0.8121 (t0) REVERT: A 256 LYS cc_start: 0.8545 (mtmm) cc_final: 0.7858 (mtmm) REVERT: A 321 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7803 (mmm-85) outliers start: 7 outliers final: 5 residues processed: 32 average time/residue: 0.1830 time to fit residues: 7.2473 Evaluate side-chains 33 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.138324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114001 restraints weight = 4207.598| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.00 r_work: 0.3244 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3154 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= 0.186 Angle : 0.525 5.547 4694 Z= 0.274 Chirality : 0.042 0.197 533 Planarity : 0.005 0.046 569 Dihedral : 4.054 13.272 455 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.42 % Allowed : 17.05 % Favored : 81.53 % 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: 1.09 (0.43), residues: 423 helix: 1.28 (0.30), residues: 333 sheet: None (None), residues: 0 loop : -1.25 (0.65), 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 0.010 0.001 TYR A 335 ARG 0.001 0.000 ARG A 195 *********************** 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 32 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.356 Fit side-chains REVERT: A 175 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8335 (tt0) REVERT: A 256 LYS cc_start: 0.8548 (mtmm) cc_final: 0.7862 (mtmm) REVERT: A 321 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7798 (mmm-85) outliers start: 5 outliers final: 5 residues processed: 29 average time/residue: 0.2104 time to fit residues: 7.5697 Evaluate side-chains 32 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 36 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 = 0.3677 r_free = 0.3677 target = 0.136589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.112174 restraints weight = 4206.838| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.00 r_work: 0.3215 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3440 Z= 0.219 Angle : 0.540 5.383 4694 Z= 0.282 Chirality : 0.042 0.183 533 Planarity : 0.005 0.047 569 Dihedral : 4.117 13.295 455 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.70 % Allowed : 17.05 % 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: 1.02 (0.43), residues: 423 helix: 1.22 (0.30), residues: 333 sheet: None (None), residues: 0 loop : -1.23 (0.65), 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 0.012 0.001 TYR A 335 ARG 0.001 0.000 ARG A 195 ********************** 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 37 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.343 Fit side-chains REVERT: A 66 ASP cc_start: 0.8845 (t70) cc_final: 0.8401 (t0) REVERT: A 175 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8365 (tt0) REVERT: A 256 LYS cc_start: 0.8564 (mtmm) cc_final: 0.7873 (mtmm) REVERT: A 321 ARG cc_start: 0.8085 (mmm-85) cc_final: 0.7819 (mmm-85) outliers start: 6 outliers final: 4 residues processed: 34 average time/residue: 0.1850 time to fit residues: 7.8320 Evaluate side-chains 35 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 443 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 0.0060 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 0.4574 ------------------------------------------------------------------------------- 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 = 0.138492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.114032 restraints weight = 4192.758| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.00 r_work: 0.3247 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3272 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= 0.169 Angle : 0.519 6.027 4694 Z= 0.270 Chirality : 0.041 0.165 533 Planarity : 0.005 0.046 569 Dihedral : 4.057 13.346 455 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.14 % Allowed : 17.61 % 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: 1.14 (0.43), residues: 423 helix: 1.24 (0.30), residues: 339 sheet: None (None), residues: 0 loop : -1.09 (0.68), 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 0.010 0.001 PHE A 299 TYR 0.010 0.001 TYR A 335 ARG 0.000 0.000 ARG A 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1969.42 seconds wall clock time: 35 minutes 57.80 seconds (2157.80 seconds total)