Starting phenix.real_space_refine on Wed Mar 5 16:39:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cah_30331/03_2025/7cah_30331.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cah_30331/03_2025/7cah_30331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cah_30331/03_2025/7cah_30331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cah_30331/03_2025/7cah_30331.map" model { file = "/net/cci-nas-00/data/ceres_data/7cah_30331/03_2025/7cah_30331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cah_30331/03_2025/7cah_30331.cif" } resolution = 3.9 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= 0.212 sd= 3.720 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 7 5.16 5 C 1842 2.51 5 N 473 2.21 5 O 567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2889 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 704 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "E" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1282 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 105 Time building chain proxies: 2.40, per 1000 atoms: 0.83 Number of scatterers: 2889 At special positions: 0 Unit cell: (68.64, 72.8, 64.48, 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 7 16.00 O 567 8.00 N 473 7.00 C 1842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 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: 0.70 Conformation dependent library (CDL) restraints added in 363.2 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 7 sheets defined 11.9% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.717A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.618A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.741A pdb=" N VAL D 12 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 18 through 22 Processing sheet with id=AA3, first strand: chain 'D' and resid 52 through 53 removed outlier: 5.155A pdb=" N SER D 42 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS D 38 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TRP D 34 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.748A pdb=" N LYS E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TRP E 47 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 96 hydrogen bonds defined for protein. 213 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: 0.67 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 923 1.34 - 1.46: 741 1.46 - 1.58: 1294 1.58 - 1.70: 0 1.70 - 1.82: 7 Bond restraints: 2965 Sorted by residual: bond pdb=" C ILE E 51 " pdb=" N ASP E 52 " ideal model delta sigma weight residual 1.330 1.269 0.061 1.47e-02 4.63e+03 1.73e+01 bond pdb=" C ASP E 102 " pdb=" N PRO E 103 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.11e+00 bond pdb=" C THR A 430 " pdb=" N GLY A 431 " ideal model delta sigma weight residual 1.328 1.338 -0.010 1.13e-02 7.83e+03 8.60e-01 bond pdb=" N CYS A 379 " pdb=" CA CYS A 379 " ideal model delta sigma weight residual 1.458 1.447 0.011 1.19e-02 7.06e+03 8.56e-01 bond pdb=" CB TRP D 93 " pdb=" CG TRP D 93 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 8.43e-01 ... (remaining 2960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 4033 3.73 - 7.45: 29 7.45 - 11.18: 1 11.18 - 14.91: 0 14.91 - 18.63: 1 Bond angle restraints: 4064 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 123.14 -8.74 2.30e+00 1.89e-01 1.44e+01 angle pdb=" C LYS A 378 " pdb=" N CYS A 379 " pdb=" CA CYS A 379 " ideal model delta sigma weight residual 123.00 118.23 4.77 1.41e+00 5.03e-01 1.14e+01 angle pdb=" C LYS E 12 " pdb=" N LYS E 13 " pdb=" CA LYS E 13 " ideal model delta sigma weight residual 120.81 139.44 -18.63 5.77e+00 3.00e-02 1.04e+01 angle pdb=" C ILE E 51 " pdb=" N ASP E 52 " pdb=" CA ASP E 52 " ideal model delta sigma weight residual 120.68 115.86 4.82 1.52e+00 4.33e-01 1.00e+01 angle pdb=" N HIS A 519 " pdb=" CA HIS A 519 " pdb=" C HIS A 519 " ideal model delta sigma weight residual 114.09 109.34 4.75 1.55e+00 4.16e-01 9.40e+00 ... (remaining 4059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 1503 15.51 - 31.02: 170 31.02 - 46.53: 33 46.53 - 62.04: 1 62.04 - 77.55: 3 Dihedral angle restraints: 1710 sinusoidal: 535 harmonic: 1175 Sorted by residual: dihedral pdb=" CA ASP E 102 " pdb=" C ASP E 102 " pdb=" N PRO E 103 " pdb=" CA PRO E 103 " ideal model delta harmonic sigma weight residual -180.00 -137.55 -42.45 0 5.00e+00 4.00e-02 7.21e+01 dihedral pdb=" CA CYS A 432 " pdb=" C CYS A 432 " pdb=" N VAL A 433 " pdb=" CA VAL A 433 " ideal model delta harmonic sigma weight residual -180.00 -149.72 -30.28 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 149.85 30.15 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 1707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 259 0.033 - 0.065: 116 0.065 - 0.098: 48 0.098 - 0.131: 23 0.131 - 0.163: 7 Chirality restraints: 453 Sorted by residual: chirality pdb=" CA CYS A 432 " pdb=" N CYS A 432 " pdb=" C CYS A 432 " pdb=" CB CYS A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA VAL D 12 " pdb=" N VAL D 12 " pdb=" C VAL D 12 " pdb=" CB VAL D 12 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 450 not shown) Planarity restraints: 531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 102 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO E 103 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 411 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO A 412 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO A 521 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.023 5.00e-02 4.00e+02 ... (remaining 528 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 127 2.69 - 3.24: 3052 3.24 - 3.79: 4383 3.79 - 4.35: 5694 4.35 - 4.90: 9144 Nonbonded interactions: 22400 Sorted by model distance: nonbonded pdb=" OG SER E 119 " pdb=" O ALA E 121 " model vdw 2.137 3.040 nonbonded pdb=" O ASP E 102 " pdb=" N TYR E 104 " model vdw 2.222 3.120 nonbonded pdb=" OD2 ASP E 60 " pdb=" NZ LYS E 65 " model vdw 2.242 3.120 nonbonded pdb=" OD1 ASN A 437 " pdb=" N SER A 438 " model vdw 2.297 3.120 nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.336 3.040 ... (remaining 22395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.740 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:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 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 : 0.005 0.061 2965 Z= 0.316 Angle : 0.921 18.632 4064 Z= 0.508 Chirality : 0.050 0.163 453 Planarity : 0.006 0.062 531 Dihedral : 13.676 77.553 951 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 19.95 % Favored : 79.80 % Rotamer: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.53 % 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: -5.76 (0.31), residues: 396 helix: -4.70 (0.25), residues: 39 sheet: -3.12 (0.39), residues: 117 loop : -4.25 (0.30), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 110 HIS 0.005 0.003 HIS A 519 PHE 0.024 0.002 PHE D 82 TYR 0.017 0.002 TYR E 32 ARG 0.003 0.001 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.339 Fit side-chains REVERT: A 340 GLU cc_start: 0.6417 (pp20) cc_final: 0.6041 (pp20) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1173 time to fit residues: 6.5696 Evaluate side-chains 24 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 30 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.091460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.086277 restraints weight = 12494.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.086616 restraints weight = 11007.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.086735 restraints weight = 9919.227| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2965 Z= 0.187 Angle : 0.727 15.894 4064 Z= 0.366 Chirality : 0.048 0.199 453 Planarity : 0.006 0.054 531 Dihedral : 6.786 47.747 430 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 2.22 % Allowed : 14.81 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -4.82 (0.34), residues: 396 helix: -3.73 (0.50), residues: 39 sheet: -2.52 (0.41), residues: 118 loop : -3.64 (0.33), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 110 HIS 0.008 0.003 HIS E 35 PHE 0.018 0.001 PHE D 82 TYR 0.011 0.002 TYR A 365 ARG 0.001 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.6608 (pp20) cc_final: 0.6214 (pp20) outliers start: 6 outliers final: 2 residues processed: 44 average time/residue: 0.1160 time to fit residues: 6.6868 Evaluate side-chains 31 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 40.0000 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.089504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.085055 restraints weight = 12442.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.085055 restraints weight = 11341.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.085056 restraints weight = 11340.613| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2965 Z= 0.261 Angle : 0.756 16.137 4064 Z= 0.384 Chirality : 0.049 0.176 453 Planarity : 0.006 0.055 531 Dihedral : 7.038 44.039 430 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.16 % Favored : 83.84 % Rotamer: Outliers : 4.44 % Allowed : 14.81 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.26 % 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: -4.61 (0.36), residues: 396 helix: -3.56 (0.62), residues: 33 sheet: -2.57 (0.40), residues: 121 loop : -3.40 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 110 HIS 0.004 0.002 HIS A 519 PHE 0.020 0.002 PHE D 82 TYR 0.011 0.001 TYR E 50 ARG 0.004 0.001 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.346 Fit side-chains REVERT: A 340 GLU cc_start: 0.6868 (pp20) cc_final: 0.6372 (pp20) outliers start: 12 outliers final: 6 residues processed: 40 average time/residue: 0.1142 time to fit residues: 6.0588 Evaluate side-chains 32 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 106 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 0.0670 chunk 5 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.090373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.085859 restraints weight = 12417.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 15)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.085890 restraints weight = 11384.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.085890 restraints weight = 11133.297| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2965 Z= 0.231 Angle : 0.725 15.815 4064 Z= 0.369 Chirality : 0.048 0.156 453 Planarity : 0.006 0.058 531 Dihedral : 6.673 44.367 430 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.13 % Favored : 86.87 % Rotamer: Outliers : 4.07 % Allowed : 17.78 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -4.32 (0.37), residues: 396 helix: -3.62 (0.54), residues: 33 sheet: -2.21 (0.43), residues: 119 loop : -3.26 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 110 HIS 0.005 0.003 HIS E 35 PHE 0.019 0.002 PHE D 82 TYR 0.010 0.001 TYR E 50 ARG 0.002 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.6686 (pp20) cc_final: 0.6235 (pp20) outliers start: 11 outliers final: 6 residues processed: 41 average time/residue: 0.1229 time to fit residues: 6.5167 Evaluate side-chains 34 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.092480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.086791 restraints weight = 12610.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.087346 restraints weight = 10606.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.087645 restraints weight = 9209.434| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2965 Z= 0.174 Angle : 0.674 14.043 4064 Z= 0.343 Chirality : 0.047 0.153 453 Planarity : 0.005 0.051 531 Dihedral : 6.109 41.021 430 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.87 % Favored : 88.13 % Rotamer: Outliers : 3.70 % Allowed : 18.89 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -4.06 (0.38), residues: 396 helix: -3.51 (0.51), residues: 39 sheet: -1.87 (0.44), residues: 120 loop : -3.13 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 110 HIS 0.005 0.002 HIS E 35 PHE 0.015 0.001 PHE D 82 TYR 0.016 0.001 TYR A 369 ARG 0.001 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.6927 (pp20) cc_final: 0.6483 (pp20) outliers start: 10 outliers final: 4 residues processed: 47 average time/residue: 0.1309 time to fit residues: 7.8412 Evaluate side-chains 37 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 106 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.1980 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.093906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.088017 restraints weight = 12298.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.088515 restraints weight = 10627.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.088795 restraints weight = 9466.726| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2965 Z= 0.162 Angle : 0.662 14.903 4064 Z= 0.333 Chirality : 0.046 0.163 453 Planarity : 0.006 0.055 531 Dihedral : 5.845 40.168 430 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 2.59 % Allowed : 20.37 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -3.74 (0.38), residues: 396 helix: -3.71 (0.53), residues: 33 sheet: -1.60 (0.44), residues: 122 loop : -2.91 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 110 HIS 0.005 0.002 HIS E 35 PHE 0.034 0.002 PHE E 54 TYR 0.010 0.001 TYR A 369 ARG 0.001 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.6671 (pp20) cc_final: 0.6287 (pp20) outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 0.1147 time to fit residues: 6.6009 Evaluate side-chains 40 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain A residue 362 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 0.0470 chunk 37 optimal weight: 0.0770 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.8038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.093488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.087252 restraints weight = 12294.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.087640 restraints weight = 10481.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.088196 restraints weight = 9364.599| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2965 Z= 0.170 Angle : 0.682 13.923 4064 Z= 0.337 Chirality : 0.046 0.158 453 Planarity : 0.005 0.056 531 Dihedral : 5.668 38.100 430 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 3.33 % Allowed : 21.11 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -3.59 (0.39), residues: 396 helix: -3.26 (0.57), residues: 39 sheet: -1.50 (0.45), residues: 123 loop : -2.84 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 110 HIS 0.004 0.002 HIS E 35 PHE 0.021 0.002 PHE E 54 TYR 0.008 0.001 TYR E 50 ARG 0.002 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.264 Fit side-chains REVERT: A 340 GLU cc_start: 0.6816 (pp20) cc_final: 0.5661 (pp20) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.1049 time to fit residues: 6.1653 Evaluate side-chains 39 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 376 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 0.0970 chunk 1 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 0.0070 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.095009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.088772 restraints weight = 12084.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.089223 restraints weight = 10650.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.089343 restraints weight = 9378.660| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 2965 Z= 0.163 Angle : 0.677 13.481 4064 Z= 0.334 Chirality : 0.047 0.158 453 Planarity : 0.006 0.056 531 Dihedral : 5.606 41.791 430 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 2.96 % Allowed : 21.85 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -3.46 (0.39), residues: 396 helix: -3.16 (0.61), residues: 39 sheet: -1.36 (0.45), residues: 122 loop : -2.77 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.002 HIS E 35 PHE 0.016 0.001 PHE E 54 TYR 0.011 0.001 TYR A 369 ARG 0.001 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.303 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.1124 time to fit residues: 6.8867 Evaluate side-chains 37 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain A residue 362 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 30 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 18 optimal weight: 0.0670 overall best weight: 1.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.091933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.086455 restraints weight = 12678.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.086808 restraints weight = 11500.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.086911 restraints weight = 10460.731| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2965 Z= 0.262 Angle : 0.743 14.251 4064 Z= 0.370 Chirality : 0.048 0.159 453 Planarity : 0.006 0.058 531 Dihedral : 6.161 41.767 430 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.65 % Favored : 85.35 % Rotamer: Outliers : 2.22 % Allowed : 24.07 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -3.56 (0.39), residues: 396 helix: -3.34 (0.61), residues: 33 sheet: -1.57 (0.44), residues: 123 loop : -2.77 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 110 HIS 0.004 0.002 HIS A 519 PHE 0.024 0.002 PHE E 54 TYR 0.011 0.002 TYR E 50 ARG 0.004 0.001 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.340 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 0.1186 time to fit residues: 6.0940 Evaluate side-chains 35 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 34 optimal weight: 0.0270 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.094285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.090132 restraints weight = 12760.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.090132 restraints weight = 11936.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.090132 restraints weight = 11936.865| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2965 Z= 0.202 Angle : 0.709 13.665 4064 Z= 0.353 Chirality : 0.047 0.158 453 Planarity : 0.006 0.061 531 Dihedral : 5.858 41.115 430 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 1.11 % Allowed : 24.44 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -3.40 (0.40), residues: 396 helix: -3.28 (0.62), residues: 33 sheet: -1.39 (0.46), residues: 125 loop : -2.71 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 110 HIS 0.004 0.002 HIS E 35 PHE 0.022 0.002 PHE E 54 TYR 0.010 0.001 TYR E 50 ARG 0.001 0.000 ARG E 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.344 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 37 average time/residue: 0.0970 time to fit residues: 5.0504 Evaluate side-chains 36 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 0.0570 chunk 14 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 15 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 30.0000 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.095767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.091125 restraints weight = 12147.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.091328 restraints weight = 11011.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.091373 restraints weight = 10280.427| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2965 Z= 0.188 Angle : 0.714 12.498 4064 Z= 0.358 Chirality : 0.047 0.170 453 Planarity : 0.006 0.060 531 Dihedral : 5.509 37.939 430 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 1.11 % Allowed : 24.07 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -3.30 (0.40), residues: 396 helix: -3.23 (0.59), residues: 39 sheet: -1.28 (0.46), residues: 127 loop : -2.62 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 110 HIS 0.004 0.002 HIS E 35 PHE 0.021 0.002 PHE E 54 TYR 0.010 0.001 TYR E 50 ARG 0.002 0.001 ARG A 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1176.87 seconds wall clock time: 21 minutes 5.83 seconds (1265.83 seconds total)