Starting phenix.real_space_refine on Wed Jul 23 17:26:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mau_63758/07_2025/9mau_63758_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mau_63758/07_2025/9mau_63758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mau_63758/07_2025/9mau_63758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mau_63758/07_2025/9mau_63758.map" model { file = "/net/cci-nas-00/data/ceres_data/9mau_63758/07_2025/9mau_63758_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mau_63758/07_2025/9mau_63758_neut.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.128 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 31 5.16 5 C 2511 2.51 5 N 657 2.21 5 O 675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3874 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3874 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 479} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 3.10, per 1000 atoms: 0.80 Number of scatterers: 3874 At special positions: 0 Unit cell: (105.316, 52.192, 68.968, 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 31 16.00 O 675 8.00 N 657 7.00 C 2511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.01 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " distance=2.03 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: 0.99 Conformation dependent library (CDL) restraints added in 447.8 milliseconds 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 932 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 2 sheets defined 80.8% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 removed outlier: 3.936A pdb=" N GLN A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 26 Processing helix chain 'A' and resid 28 through 36 removed outlier: 4.423A pdb=" N ALA A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 40 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 62 through 67 removed outlier: 4.084A pdb=" N TRP A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 131 through 160 removed outlier: 4.326A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 181 Processing helix chain 'A' and resid 184 through 213 removed outlier: 3.602A pdb=" N MET A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 218 through 244 removed outlier: 3.601A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 256 through 265 removed outlier: 4.067A pdb=" N ALA A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.535A pdb=" N ALA A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 332 removed outlier: 3.903A pdb=" N LEU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 358 removed outlier: 3.584A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 393 removed outlier: 3.616A pdb=" N ASP A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix removed outlier: 3.562A pdb=" N LEU A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 415 removed outlier: 3.700A pdb=" N ALA A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 449 removed outlier: 3.574A pdb=" N ARG A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 453 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 484 through 501 Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 515 through 522 removed outlier: 3.505A pdb=" N LEU A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 268 hydrogen bonds defined for protein. 795 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: 1.18 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 603 1.31 - 1.44: 1076 1.44 - 1.56: 2236 1.56 - 1.69: 1 1.69 - 1.81: 49 Bond restraints: 3965 Sorted by residual: bond pdb=" C CYS A 128 " pdb=" O CYS A 128 " ideal model delta sigma weight residual 1.243 1.206 0.038 9.50e-03 1.11e+04 1.57e+01 bond pdb=" C SER A 472 " pdb=" O SER A 472 " ideal model delta sigma weight residual 1.244 1.204 0.039 1.00e-02 1.00e+04 1.54e+01 bond pdb=" C THR A 424 " pdb=" O THR A 424 " ideal model delta sigma weight residual 1.237 1.191 0.045 1.16e-02 7.43e+03 1.52e+01 bond pdb=" C PHE A 339 " pdb=" O PHE A 339 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.15e-02 7.56e+03 1.44e+01 bond pdb=" C GLN A 20 " pdb=" O GLN A 20 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.39e+01 ... (remaining 3960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 4695 1.86 - 3.71: 576 3.71 - 5.57: 90 5.57 - 7.43: 25 7.43 - 9.29: 13 Bond angle restraints: 5399 Sorted by residual: angle pdb=" N SER A 77 " pdb=" CA SER A 77 " pdb=" C SER A 77 " ideal model delta sigma weight residual 111.36 118.89 -7.53 1.09e+00 8.42e-01 4.77e+01 angle pdb=" N ASN A 412 " pdb=" CA ASN A 412 " pdb=" C ASN A 412 " ideal model delta sigma weight residual 111.69 103.39 8.30 1.23e+00 6.61e-01 4.55e+01 angle pdb=" N ASP A 5 " pdb=" CA ASP A 5 " pdb=" C ASP A 5 " ideal model delta sigma weight residual 113.41 105.41 8.00 1.22e+00 6.72e-01 4.30e+01 angle pdb=" N PHE A 259 " pdb=" CA PHE A 259 " pdb=" C PHE A 259 " ideal model delta sigma weight residual 112.90 105.03 7.87 1.31e+00 5.83e-01 3.61e+01 angle pdb=" N VAL A 143 " pdb=" CA VAL A 143 " pdb=" C VAL A 143 " ideal model delta sigma weight residual 110.62 104.52 6.10 1.02e+00 9.61e-01 3.58e+01 ... (remaining 5394 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.59: 2183 17.59 - 35.17: 129 35.17 - 52.75: 23 52.75 - 70.33: 4 70.33 - 87.91: 3 Dihedral angle restraints: 2342 sinusoidal: 891 harmonic: 1451 Sorted by residual: dihedral pdb=" C VAL A 164 " pdb=" N VAL A 164 " pdb=" CA VAL A 164 " pdb=" CB VAL A 164 " ideal model delta harmonic sigma weight residual -122.00 -131.58 9.58 0 2.50e+00 1.60e-01 1.47e+01 dihedral pdb=" C VAL A 428 " pdb=" N VAL A 428 " pdb=" CA VAL A 428 " pdb=" CB VAL A 428 " ideal model delta harmonic sigma weight residual -122.00 -130.23 8.23 0 2.50e+00 1.60e-01 1.08e+01 dihedral pdb=" C PHE A 152 " pdb=" N PHE A 152 " pdb=" CA PHE A 152 " pdb=" CB PHE A 152 " ideal model delta harmonic sigma weight residual -122.60 -130.68 8.08 0 2.50e+00 1.60e-01 1.05e+01 ... (remaining 2339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 424 0.073 - 0.145: 144 0.145 - 0.218: 49 0.218 - 0.291: 10 0.291 - 0.364: 3 Chirality restraints: 630 Sorted by residual: chirality pdb=" CA PHE A 152 " pdb=" N PHE A 152 " pdb=" C PHE A 152 " pdb=" CB PHE A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA TYR A 354 " pdb=" N TYR A 354 " pdb=" C TYR A 354 " pdb=" CB TYR A 354 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB VAL A 127 " pdb=" CA VAL A 127 " pdb=" CG1 VAL A 127 " pdb=" CG2 VAL A 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 627 not shown) Planarity restraints: 679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " -0.047 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO A 27 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 493 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO A 494 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 494 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 494 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 499 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C ALA A 499 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA A 499 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A 500 " 0.013 2.00e-02 2.50e+03 ... (remaining 676 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1531 2.90 - 3.40: 4037 3.40 - 3.90: 6783 3.90 - 4.40: 7911 4.40 - 4.90: 12542 Nonbonded interactions: 32804 Sorted by model distance: nonbonded pdb=" N HIS A 48 " pdb=" O HIS A 48 " model vdw 2.403 2.496 nonbonded pdb=" N THR A 119 " pdb=" O THR A 119 " model vdw 2.406 2.496 nonbonded pdb=" N GLY A 14 " pdb=" O GLY A 14 " model vdw 2.522 2.496 nonbonded pdb=" N ASN A 39 " pdb=" N PHE A 40 " model vdw 2.548 2.560 nonbonded pdb=" N ASP A 5 " pdb=" N LEU A 6 " model vdw 2.552 2.560 ... (remaining 32799 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: 56.710 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.080 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: 0.010 Load rotamer database and sin/cos tables:44.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 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 : 0.010 0.046 3967 Z= 0.786 Angle : 1.386 9.286 5403 Z= 0.937 Chirality : 0.085 0.364 630 Planarity : 0.008 0.072 679 Dihedral : 12.107 87.915 1404 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.36), residues: 500 helix: -0.63 (0.25), residues: 373 sheet: -0.13 (1.48), residues: 10 loop : 0.64 (0.56), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 346 HIS 0.007 0.002 HIS A 246 PHE 0.019 0.003 PHE A 351 TYR 0.024 0.003 TYR A 264 ARG 0.009 0.001 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.22378 ( 268) hydrogen bonds : angle 8.04680 ( 795) SS BOND : bond 0.01679 ( 2) SS BOND : angle 1.41856 ( 4) covalent geometry : bond 0.01045 ( 3965) covalent geometry : angle 1.38622 ( 5399) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.466 Fit side-chains REVERT: A 286 ARG cc_start: 0.5987 (mtt180) cc_final: 0.5658 (mtm180) REVERT: A 327 MET cc_start: 0.7010 (mmm) cc_final: 0.5822 (ttp) REVERT: A 331 ARG cc_start: 0.6445 (ttt180) cc_final: 0.6182 (ttt-90) REVERT: A 358 MET cc_start: 0.7283 (mmm) cc_final: 0.7038 (mmm) REVERT: A 415 ILE cc_start: 0.7409 (mt) cc_final: 0.7176 (mt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.9841 time to fit residues: 86.9167 Evaluate side-chains 58 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 39 ASN A 217 HIS A 417 GLN A 455 GLN A 510 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.111012 restraints weight = 3959.932| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.09 r_work: 0.2970 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3967 Z= 0.173 Angle : 0.609 6.550 5403 Z= 0.325 Chirality : 0.040 0.146 630 Planarity : 0.006 0.050 679 Dihedral : 4.304 15.722 546 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.22 % Allowed : 7.30 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.38), residues: 500 helix: 0.94 (0.27), residues: 366 sheet: -0.82 (1.44), residues: 10 loop : 1.12 (0.58), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 274 HIS 0.004 0.002 HIS A 337 PHE 0.017 0.002 PHE A 351 TYR 0.022 0.002 TYR A 264 ARG 0.010 0.001 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.05875 ( 268) hydrogen bonds : angle 4.92950 ( 795) SS BOND : bond 0.00912 ( 2) SS BOND : angle 1.11083 ( 4) covalent geometry : bond 0.00397 ( 3965) covalent geometry : angle 0.60798 ( 5399) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.401 Fit side-chains REVERT: A 327 MET cc_start: 0.7259 (mmm) cc_final: 0.6056 (tmt) REVERT: A 394 ARG cc_start: 0.7850 (tpp-160) cc_final: 0.7625 (mtt90) REVERT: A 452 MET cc_start: 0.5757 (OUTLIER) cc_final: 0.5318 (ppp) outliers start: 5 outliers final: 1 residues processed: 48 average time/residue: 1.2749 time to fit residues: 63.7359 Evaluate side-chains 44 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 452 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 0.0370 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.0570 chunk 18 optimal weight: 0.9980 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 GLN A 455 GLN A 510 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.149931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.111582 restraints weight = 3934.350| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.09 r_work: 0.2988 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3967 Z= 0.134 Angle : 0.536 5.567 5403 Z= 0.275 Chirality : 0.037 0.125 630 Planarity : 0.005 0.042 679 Dihedral : 4.113 14.014 546 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.70 % Allowed : 9.49 % Favored : 88.81 % 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: 1.96 (0.38), residues: 500 helix: 1.53 (0.27), residues: 366 sheet: -1.77 (1.42), residues: 10 loop : 1.17 (0.61), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 247 HIS 0.003 0.001 HIS A 47 PHE 0.014 0.001 PHE A 351 TYR 0.021 0.002 TYR A 444 ARG 0.006 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.04722 ( 268) hydrogen bonds : angle 4.34421 ( 795) SS BOND : bond 0.00717 ( 2) SS BOND : angle 0.78963 ( 4) covalent geometry : bond 0.00295 ( 3965) covalent geometry : angle 0.53596 ( 5399) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.402 Fit side-chains REVERT: A 34 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.8068 (m-70) REVERT: A 273 ARG cc_start: 0.6397 (OUTLIER) cc_final: 0.5556 (mmp80) REVERT: A 300 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6395 (mm-30) REVERT: A 327 MET cc_start: 0.7276 (mmm) cc_final: 0.6027 (tmt) REVERT: A 328 GLU cc_start: 0.6697 (tt0) cc_final: 0.6491 (tt0) REVERT: A 452 MET cc_start: 0.5651 (ptm) cc_final: 0.5368 (ppp) outliers start: 7 outliers final: 1 residues processed: 53 average time/residue: 1.2997 time to fit residues: 71.2775 Evaluate side-chains 45 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 273 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.0040 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 455 GLN A 510 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.150122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.111858 restraints weight = 4006.073| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.09 r_work: 0.2986 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3967 Z= 0.124 Angle : 0.509 5.095 5403 Z= 0.260 Chirality : 0.037 0.118 630 Planarity : 0.005 0.038 679 Dihedral : 3.948 14.218 546 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.68 % Allowed : 9.25 % Favored : 88.08 % 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: 2.06 (0.38), residues: 500 helix: 1.67 (0.27), residues: 365 sheet: -1.76 (1.32), residues: 10 loop : 1.01 (0.59), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 274 HIS 0.003 0.001 HIS A 337 PHE 0.015 0.001 PHE A 351 TYR 0.017 0.002 TYR A 264 ARG 0.006 0.001 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.04443 ( 268) hydrogen bonds : angle 4.17512 ( 795) SS BOND : bond 0.00607 ( 2) SS BOND : angle 0.68971 ( 4) covalent geometry : bond 0.00269 ( 3965) covalent geometry : angle 0.50931 ( 5399) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.384 Fit side-chains REVERT: A 9 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6569 (tp-100) REVERT: A 34 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7983 (m-70) REVERT: A 300 GLU cc_start: 0.6607 (mm-30) cc_final: 0.6240 (mm-30) REVERT: A 327 MET cc_start: 0.7204 (mmm) cc_final: 0.5923 (tmt) REVERT: A 452 MET cc_start: 0.5777 (OUTLIER) cc_final: 0.5506 (ppp) outliers start: 11 outliers final: 2 residues processed: 54 average time/residue: 1.1025 time to fit residues: 61.8169 Evaluate side-chains 49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 452 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN A 510 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.147966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.109816 restraints weight = 4098.091| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.11 r_work: 0.2961 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3967 Z= 0.143 Angle : 0.519 5.212 5403 Z= 0.262 Chirality : 0.038 0.125 630 Planarity : 0.004 0.037 679 Dihedral : 3.913 14.349 546 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.46 % Allowed : 11.19 % Favored : 87.35 % 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: 2.02 (0.38), residues: 500 helix: 1.64 (0.27), residues: 372 sheet: -1.94 (1.35), residues: 10 loop : 0.94 (0.60), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 274 HIS 0.003 0.001 HIS A 337 PHE 0.016 0.001 PHE A 351 TYR 0.019 0.002 TYR A 444 ARG 0.004 0.000 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 268) hydrogen bonds : angle 4.15360 ( 795) SS BOND : bond 0.00731 ( 2) SS BOND : angle 0.62292 ( 4) covalent geometry : bond 0.00335 ( 3965) covalent geometry : angle 0.51848 ( 5399) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.381 Fit side-chains REVERT: A 9 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6640 (tp-100) REVERT: A 327 MET cc_start: 0.7175 (mmm) cc_final: 0.5941 (tmt) REVERT: A 452 MET cc_start: 0.6010 (ptm) cc_final: 0.5688 (ppp) outliers start: 6 outliers final: 3 residues processed: 45 average time/residue: 0.9262 time to fit residues: 43.6476 Evaluate side-chains 43 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 443 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN A 510 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.145539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.107760 restraints weight = 3995.843| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.07 r_work: 0.2935 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 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 : 0.004 0.036 3967 Z= 0.151 Angle : 0.521 5.240 5403 Z= 0.264 Chirality : 0.038 0.117 630 Planarity : 0.004 0.036 679 Dihedral : 3.878 14.470 546 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.70 % Allowed : 11.19 % Favored : 87.10 % 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: 2.08 (0.38), residues: 500 helix: 1.70 (0.27), residues: 372 sheet: -1.96 (1.26), residues: 10 loop : 0.89 (0.60), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 274 HIS 0.004 0.001 HIS A 337 PHE 0.016 0.002 PHE A 351 TYR 0.019 0.002 TYR A 444 ARG 0.004 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.04581 ( 268) hydrogen bonds : angle 4.13327 ( 795) SS BOND : bond 0.00754 ( 2) SS BOND : angle 0.53454 ( 4) covalent geometry : bond 0.00357 ( 3965) covalent geometry : angle 0.52051 ( 5399) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.426 Fit side-chains REVERT: A 6 LEU cc_start: 0.5374 (OUTLIER) cc_final: 0.5102 (mp) REVERT: A 9 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6740 (tp-100) REVERT: A 286 ARG cc_start: 0.5991 (mtt180) cc_final: 0.5620 (mtm180) REVERT: A 327 MET cc_start: 0.7165 (mmm) cc_final: 0.5964 (tmt) REVERT: A 331 ARG cc_start: 0.7140 (ttt180) cc_final: 0.6722 (ttp80) REVERT: A 443 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6117 (mp) REVERT: A 452 MET cc_start: 0.6240 (OUTLIER) cc_final: 0.5925 (ppp) outliers start: 7 outliers final: 1 residues processed: 52 average time/residue: 1.2483 time to fit residues: 67.2350 Evaluate side-chains 49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 46 optimal weight: 0.0060 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.147959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.110287 restraints weight = 3961.404| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.05 r_work: 0.2967 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3967 Z= 0.120 Angle : 0.492 5.320 5403 Z= 0.249 Chirality : 0.036 0.118 630 Planarity : 0.004 0.035 679 Dihedral : 3.768 14.200 546 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.46 % Allowed : 11.68 % Favored : 86.86 % 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: 2.31 (0.38), residues: 500 helix: 1.89 (0.27), residues: 372 sheet: -1.88 (1.34), residues: 10 loop : 0.91 (0.61), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 274 HIS 0.003 0.001 HIS A 337 PHE 0.015 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.003 0.000 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 268) hydrogen bonds : angle 4.05480 ( 795) SS BOND : bond 0.00550 ( 2) SS BOND : angle 0.55984 ( 4) covalent geometry : bond 0.00264 ( 3965) covalent geometry : angle 0.49157 ( 5399) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.382 Fit side-chains REVERT: A 9 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6749 (tp-100) REVERT: A 273 ARG cc_start: 0.6541 (mtp85) cc_final: 0.6199 (mmp80) REVERT: A 286 ARG cc_start: 0.5887 (mtt180) cc_final: 0.5526 (mtm180) REVERT: A 327 MET cc_start: 0.7140 (mmm) cc_final: 0.5918 (tmt) REVERT: A 331 ARG cc_start: 0.7144 (ttt180) cc_final: 0.6709 (ttp80) REVERT: A 443 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6186 (mp) REVERT: A 452 MET cc_start: 0.6244 (ptm) cc_final: 0.5955 (ppp) outliers start: 6 outliers final: 1 residues processed: 52 average time/residue: 1.0945 time to fit residues: 59.0792 Evaluate side-chains 49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 443 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 0.0060 chunk 3 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.148079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.110442 restraints weight = 3988.716| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.05 r_work: 0.2968 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3967 Z= 0.120 Angle : 0.489 5.316 5403 Z= 0.247 Chirality : 0.036 0.118 630 Planarity : 0.004 0.035 679 Dihedral : 3.699 14.101 546 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.70 % Allowed : 12.41 % Favored : 85.89 % 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: 2.37 (0.38), residues: 500 helix: 1.92 (0.27), residues: 372 sheet: -1.88 (1.36), residues: 10 loop : 0.99 (0.62), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 274 HIS 0.006 0.001 HIS A 34 PHE 0.015 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.004 0.000 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 268) hydrogen bonds : angle 4.03714 ( 795) SS BOND : bond 0.00552 ( 2) SS BOND : angle 0.48471 ( 4) covalent geometry : bond 0.00264 ( 3965) covalent geometry : angle 0.48909 ( 5399) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.471 Fit side-chains REVERT: A 6 LEU cc_start: 0.5217 (OUTLIER) cc_final: 0.4981 (mp) REVERT: A 9 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6686 (tp-100) REVERT: A 127 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.7495 (m) REVERT: A 273 ARG cc_start: 0.6543 (mtp85) cc_final: 0.6211 (mmp80) REVERT: A 286 ARG cc_start: 0.5848 (mtt180) cc_final: 0.5386 (mtm180) REVERT: A 327 MET cc_start: 0.7157 (mmm) cc_final: 0.5940 (tmt) REVERT: A 331 ARG cc_start: 0.7117 (ttt180) cc_final: 0.6730 (ttp80) REVERT: A 390 ASN cc_start: 0.6854 (m110) cc_final: 0.6512 (m-40) REVERT: A 443 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6161 (mp) REVERT: A 452 MET cc_start: 0.6219 (OUTLIER) cc_final: 0.5935 (ppp) outliers start: 7 outliers final: 2 residues processed: 48 average time/residue: 1.5370 time to fit residues: 77.3431 Evaluate side-chains 52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.150762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113092 restraints weight = 3986.772| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.07 r_work: 0.3002 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3967 Z= 0.105 Angle : 0.472 5.298 5403 Z= 0.237 Chirality : 0.035 0.120 630 Planarity : 0.004 0.035 679 Dihedral : 3.572 13.778 546 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.22 % Allowed : 13.63 % Favored : 85.16 % 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: 2.54 (0.38), residues: 500 helix: 2.06 (0.27), residues: 371 sheet: -1.89 (1.38), residues: 10 loop : 0.99 (0.62), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 274 HIS 0.005 0.001 HIS A 34 PHE 0.015 0.001 PHE A 351 TYR 0.015 0.001 TYR A 264 ARG 0.003 0.000 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 268) hydrogen bonds : angle 3.97039 ( 795) SS BOND : bond 0.00417 ( 2) SS BOND : angle 0.55238 ( 4) covalent geometry : bond 0.00218 ( 3965) covalent geometry : angle 0.47164 ( 5399) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.455 Fit side-chains REVERT: A 9 GLN cc_start: 0.7133 (tt0) cc_final: 0.6709 (tp-100) REVERT: A 273 ARG cc_start: 0.6528 (mtp85) cc_final: 0.6219 (mmp80) REVERT: A 286 ARG cc_start: 0.5884 (mtt180) cc_final: 0.5444 (mtm180) REVERT: A 327 MET cc_start: 0.7135 (mmm) cc_final: 0.5910 (tmt) REVERT: A 331 ARG cc_start: 0.7111 (ttt180) cc_final: 0.6733 (ttp80) REVERT: A 443 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6164 (mp) REVERT: A 452 MET cc_start: 0.6150 (ptm) cc_final: 0.5878 (ppp) outliers start: 5 outliers final: 1 residues processed: 48 average time/residue: 1.3400 time to fit residues: 67.0286 Evaluate side-chains 45 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 443 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 0.0060 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.149385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.112090 restraints weight = 4013.875| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.05 r_work: 0.2988 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3967 Z= 0.112 Angle : 0.490 6.746 5403 Z= 0.244 Chirality : 0.036 0.118 630 Planarity : 0.004 0.034 679 Dihedral : 3.544 13.889 546 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.97 % Allowed : 13.63 % Favored : 85.40 % 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: 2.52 (0.38), residues: 500 helix: 2.02 (0.27), residues: 372 sheet: -1.82 (1.41), residues: 10 loop : 1.06 (0.62), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 274 HIS 0.005 0.001 HIS A 34 PHE 0.015 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.003 0.000 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 268) hydrogen bonds : angle 3.99389 ( 795) SS BOND : bond 0.00493 ( 2) SS BOND : angle 0.70237 ( 4) covalent geometry : bond 0.00242 ( 3965) covalent geometry : angle 0.48973 ( 5399) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.391 Fit side-chains REVERT: A 9 GLN cc_start: 0.7175 (tt0) cc_final: 0.6707 (tp-100) REVERT: A 273 ARG cc_start: 0.6525 (mtp85) cc_final: 0.6200 (mmp80) REVERT: A 286 ARG cc_start: 0.5886 (mtt180) cc_final: 0.5449 (mtm180) REVERT: A 327 MET cc_start: 0.7150 (mmm) cc_final: 0.5899 (tmt) REVERT: A 443 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6134 (mp) REVERT: A 452 MET cc_start: 0.6168 (ptm) cc_final: 0.5961 (ppp) outliers start: 4 outliers final: 2 residues processed: 45 average time/residue: 1.1492 time to fit residues: 53.7410 Evaluate side-chains 44 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 443 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN A 455 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.152138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.114061 restraints weight = 3912.578| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.09 r_work: 0.3001 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3967 Z= 0.117 Angle : 0.494 6.475 5403 Z= 0.246 Chirality : 0.036 0.118 630 Planarity : 0.004 0.034 679 Dihedral : 3.536 13.964 546 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.46 % Allowed : 12.65 % Favored : 85.89 % 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: 2.52 (0.38), residues: 500 helix: 2.01 (0.27), residues: 373 sheet: -1.74 (1.43), residues: 10 loop : 1.08 (0.62), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 274 HIS 0.005 0.001 HIS A 34 PHE 0.015 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.003 0.000 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 268) hydrogen bonds : angle 3.99462 ( 795) SS BOND : bond 0.00522 ( 2) SS BOND : angle 0.68779 ( 4) covalent geometry : bond 0.00259 ( 3965) covalent geometry : angle 0.49386 ( 5399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3779.73 seconds wall clock time: 67 minutes 38.93 seconds (4058.93 seconds total)