Starting phenix.real_space_refine on Wed Jun 4 15:11:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wef_32449/06_2025/7wef_32449.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wef_32449/06_2025/7wef_32449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wef_32449/06_2025/7wef_32449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wef_32449/06_2025/7wef_32449.map" model { file = "/net/cci-nas-00/data/ceres_data/7wef_32449/06_2025/7wef_32449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wef_32449/06_2025/7wef_32449.cif" } resolution = 3.8 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2119 2.51 5 N 565 2.21 5 O 629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3328 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Time building chain proxies: 3.36, per 1000 atoms: 1.01 Number of scatterers: 3328 At special positions: 0 Unit cell: (79.18, 85.6, 86.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 629 8.00 N 565 7.00 C 2119 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " 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: 0.76 Conformation dependent library (CDL) restraints added in 404.0 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 782 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 7.2% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.672A pdb=" N HIS C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.993A pdb=" N THR C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 366 through 371 removed outlier: 3.776A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 3.940A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA E 411 " --> pdb=" O ARG E 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 removed outlier: 4.209A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR C 79 " --> pdb=" O THR C 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.346A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.993A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.584A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.041A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.528A pdb=" N ALA L 91 " --> pdb=" O VAL L 102 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL L 102 " --> pdb=" O ALA L 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.557A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) 87 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: 0.86 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1066 1.35 - 1.47: 943 1.47 - 1.59: 1395 1.59 - 1.71: 0 1.71 - 1.84: 18 Bond restraints: 3422 Sorted by residual: bond pdb=" N LEU C 104 " pdb=" CA LEU C 104 " ideal model delta sigma weight residual 1.465 1.452 0.013 1.31e-02 5.83e+03 9.85e-01 bond pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " ideal model delta sigma weight residual 1.808 1.837 -0.029 3.30e-02 9.18e+02 7.49e-01 bond pdb=" CA THR E 333 " pdb=" CB THR E 333 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.96e-01 bond pdb=" CA ILE L 76 " pdb=" CB ILE L 76 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.36e-02 5.41e+03 6.45e-01 bond pdb=" CB TRP C 47 " pdb=" CG TRP C 47 " ideal model delta sigma weight residual 1.498 1.475 0.023 3.10e-02 1.04e+03 5.72e-01 ... (remaining 3417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 4315 1.04 - 2.07: 254 2.07 - 3.11: 60 3.11 - 4.14: 29 4.14 - 5.18: 4 Bond angle restraints: 4662 Sorted by residual: angle pdb=" C ARG C 64 " pdb=" N ASP C 65 " pdb=" CA ASP C 65 " ideal model delta sigma weight residual 121.54 126.02 -4.48 1.91e+00 2.74e-01 5.51e+00 angle pdb=" C ILE E 332 " pdb=" N THR E 333 " pdb=" CA THR E 333 " ideal model delta sigma weight residual 121.54 125.79 -4.25 1.91e+00 2.74e-01 4.95e+00 angle pdb=" CA PHE C 107 " pdb=" C PHE C 107 " pdb=" N ASP C 108 " ideal model delta sigma weight residual 115.29 117.80 -2.51 1.18e+00 7.18e-01 4.54e+00 angle pdb=" C MET C 69 " pdb=" CA MET C 69 " pdb=" CB MET C 69 " ideal model delta sigma weight residual 110.24 113.20 -2.96 1.46e+00 4.69e-01 4.10e+00 angle pdb=" CA PHE C 107 " pdb=" C PHE C 107 " pdb=" O PHE C 107 " ideal model delta sigma weight residual 122.36 119.97 2.39 1.21e+00 6.83e-01 3.91e+00 ... (remaining 4657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 1805 16.33 - 32.66: 148 32.66 - 48.99: 38 48.99 - 65.32: 4 65.32 - 81.65: 5 Dihedral angle restraints: 2000 sinusoidal: 763 harmonic: 1237 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 159.95 -66.95 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CA ILE C 51 " pdb=" C ILE C 51 " pdb=" N ASN C 52 " pdb=" CA ASN C 52 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP E 428 " pdb=" C ASP E 428 " pdb=" N PHE E 429 " pdb=" CA PHE E 429 " ideal model delta harmonic sigma weight residual -180.00 -163.76 -16.24 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 278 0.030 - 0.060: 143 0.060 - 0.090: 51 0.090 - 0.120: 19 0.120 - 0.150: 5 Chirality restraints: 496 Sorted by residual: chirality pdb=" CA ILE C 51 " pdb=" N ILE C 51 " pdb=" C ILE C 51 " pdb=" CB ILE C 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE L 20 " pdb=" N ILE L 20 " pdb=" C ILE L 20 " pdb=" CB ILE L 20 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE E 434 " pdb=" N ILE E 434 " pdb=" C ILE E 434 " pdb=" CB ILE E 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 493 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 47 " 0.012 2.00e-02 2.50e+03 1.66e-02 6.86e+00 pdb=" CG TRP C 47 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP C 47 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 47 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 47 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 47 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 47 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 47 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 47 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 47 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 72 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO C 73 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 73 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 73 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 108 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO C 109 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 109 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 109 " 0.019 5.00e-02 4.00e+02 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 592 2.77 - 3.30: 2922 3.30 - 3.84: 4973 3.84 - 4.37: 5725 4.37 - 4.90: 10342 Nonbonded interactions: 24554 Sorted by model distance: nonbonded pdb=" ND2 ASN E 439 " pdb=" OE1 GLN E 506 " model vdw 2.239 3.120 nonbonded pdb=" OG1 THR C 28 " pdb=" OG SER C 31 " model vdw 2.300 3.040 nonbonded pdb=" O THR C 28 " pdb=" OG SER C 31 " model vdw 2.309 3.040 nonbonded pdb=" O ASN L 53 " pdb=" NH1 ARG L 55 " model vdw 2.313 3.120 nonbonded pdb=" OH TYR E 369 " pdb=" O PRO E 384 " model vdw 2.326 3.040 ... (remaining 24549 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.020 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 : 0.003 0.029 3428 Z= 0.152 Angle : 0.627 5.176 4674 Z= 0.336 Chirality : 0.043 0.150 496 Planarity : 0.004 0.037 604 Dihedral : 12.721 81.647 1200 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.41), residues: 426 helix: -3.97 (0.48), residues: 26 sheet: 0.64 (0.49), residues: 135 loop : -1.38 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 47 HIS 0.002 0.001 HIS E 505 PHE 0.012 0.002 PHE E 374 TYR 0.015 0.001 TYR E 453 ARG 0.004 0.001 ARG E 509 Details of bonding type rmsd hydrogen bonds : bond 0.18861 ( 82) hydrogen bonds : angle 6.38883 ( 213) SS BOND : bond 0.00354 ( 6) SS BOND : angle 1.35629 ( 12) covalent geometry : bond 0.00332 ( 3422) covalent geometry : angle 0.62392 ( 4662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.377 Fit side-chains REVERT: C 106 TRP cc_start: 0.8053 (p-90) cc_final: 0.7845 (p-90) REVERT: E 346 ARG cc_start: 0.7386 (ttp80) cc_final: 0.6968 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1480 time to fit residues: 11.1251 Evaluate side-chains 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 33 optimal weight: 0.0370 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 39 optimal weight: 3.9990 overall best weight: 0.4054 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.141948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118026 restraints weight = 4578.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121221 restraints weight = 2904.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123675 restraints weight = 2096.834| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3428 Z= 0.119 Angle : 0.571 5.327 4674 Z= 0.297 Chirality : 0.042 0.160 496 Planarity : 0.004 0.037 604 Dihedral : 4.504 16.939 474 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.12 % Allowed : 8.38 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.41), residues: 426 helix: -3.82 (0.51), residues: 27 sheet: 0.89 (0.49), residues: 133 loop : -1.26 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 103 HIS 0.001 0.001 HIS E 505 PHE 0.009 0.001 PHE C 63 TYR 0.008 0.001 TYR L 50 ARG 0.003 0.000 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 82) hydrogen bonds : angle 5.50738 ( 213) SS BOND : bond 0.00314 ( 6) SS BOND : angle 1.44262 ( 12) covalent geometry : bond 0.00274 ( 3422) covalent geometry : angle 0.56753 ( 4662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.405 Fit side-chains REVERT: E 346 ARG cc_start: 0.7459 (ttp80) cc_final: 0.7150 (ptm-80) REVERT: E 406 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7785 (tt0) outliers start: 4 outliers final: 3 residues processed: 63 average time/residue: 0.1682 time to fit residues: 12.9693 Evaluate side-chains 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.136885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113449 restraints weight = 4640.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116286 restraints weight = 3060.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.118432 restraints weight = 2264.958| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3428 Z= 0.190 Angle : 0.629 5.330 4674 Z= 0.325 Chirality : 0.044 0.155 496 Planarity : 0.004 0.035 604 Dihedral : 4.777 17.992 474 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.96 % Allowed : 10.89 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.40), residues: 426 helix: -3.24 (0.72), residues: 21 sheet: 0.75 (0.48), residues: 133 loop : -1.50 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP L 101 HIS 0.004 0.001 HIS E 505 PHE 0.017 0.002 PHE E 429 TYR 0.010 0.002 TYR E 453 ARG 0.002 0.000 ARG E 498 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 82) hydrogen bonds : angle 5.42316 ( 213) SS BOND : bond 0.00216 ( 6) SS BOND : angle 1.51150 ( 12) covalent geometry : bond 0.00450 ( 3422) covalent geometry : angle 0.62488 ( 4662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.392 Fit side-chains REVERT: E 346 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7185 (ptm-80) outliers start: 7 outliers final: 6 residues processed: 58 average time/residue: 0.1595 time to fit residues: 11.5017 Evaluate side-chains 57 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain L residue 110 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.149466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.128328 restraints weight = 4720.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130987 restraints weight = 3262.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.132679 restraints weight = 2491.745| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3428 Z= 0.154 Angle : 0.588 5.208 4674 Z= 0.305 Chirality : 0.043 0.158 496 Planarity : 0.004 0.033 604 Dihedral : 4.696 21.157 474 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.79 % Allowed : 13.13 % Favored : 84.08 % 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: -1.29 (0.40), residues: 426 helix: -3.19 (0.72), residues: 21 sheet: 0.71 (0.48), residues: 133 loop : -1.57 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 106 HIS 0.003 0.001 HIS E 505 PHE 0.012 0.002 PHE E 429 TYR 0.010 0.001 TYR E 423 ARG 0.002 0.000 ARG E 498 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 82) hydrogen bonds : angle 5.22294 ( 213) SS BOND : bond 0.00248 ( 6) SS BOND : angle 1.30046 ( 12) covalent geometry : bond 0.00366 ( 3422) covalent geometry : angle 0.58520 ( 4662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.408 Fit side-chains REVERT: E 346 ARG cc_start: 0.7412 (ttp80) cc_final: 0.7185 (ptm-80) outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.1409 time to fit residues: 11.3737 Evaluate side-chains 63 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 110 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.0270 chunk 37 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 0.0370 overall best weight: 0.3114 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.140021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116506 restraints weight = 4635.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.119630 restraints weight = 3026.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.121842 restraints weight = 2218.585| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3428 Z= 0.107 Angle : 0.555 5.397 4674 Z= 0.286 Chirality : 0.042 0.163 496 Planarity : 0.004 0.032 604 Dihedral : 4.401 21.852 474 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.96 % Allowed : 14.25 % Favored : 83.80 % 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 (0.40), residues: 426 helix: -3.13 (0.78), residues: 21 sheet: 0.47 (0.47), residues: 141 loop : -1.46 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 106 HIS 0.001 0.001 HIS C 35 PHE 0.011 0.001 PHE C 63 TYR 0.008 0.001 TYR L 50 ARG 0.001 0.000 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 82) hydrogen bonds : angle 4.85758 ( 213) SS BOND : bond 0.00240 ( 6) SS BOND : angle 1.02178 ( 12) covalent geometry : bond 0.00262 ( 3422) covalent geometry : angle 0.55313 ( 4662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.307 Fit side-chains REVERT: E 346 ARG cc_start: 0.7510 (ttp80) cc_final: 0.7252 (ptm-80) outliers start: 7 outliers final: 7 residues processed: 66 average time/residue: 0.1363 time to fit residues: 11.2890 Evaluate side-chains 61 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.110832 restraints weight = 4867.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.113749 restraints weight = 3212.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115881 restraints weight = 2377.914| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3428 Z= 0.184 Angle : 0.620 5.282 4674 Z= 0.321 Chirality : 0.044 0.148 496 Planarity : 0.004 0.032 604 Dihedral : 4.821 25.838 474 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.35 % Allowed : 13.13 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.40), residues: 426 helix: -3.05 (0.82), residues: 21 sheet: 0.17 (0.46), residues: 150 loop : -1.54 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 106 HIS 0.003 0.001 HIS E 505 PHE 0.016 0.002 PHE E 429 TYR 0.010 0.001 TYR E 453 ARG 0.001 0.000 ARG E 509 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 82) hydrogen bonds : angle 4.99843 ( 213) SS BOND : bond 0.00172 ( 6) SS BOND : angle 1.33849 ( 12) covalent geometry : bond 0.00441 ( 3422) covalent geometry : angle 0.61670 ( 4662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.337 Fit side-chains REVERT: E 346 ARG cc_start: 0.7498 (ttp80) cc_final: 0.7254 (ptm-80) outliers start: 12 outliers final: 9 residues processed: 61 average time/residue: 0.1217 time to fit residues: 9.5889 Evaluate side-chains 62 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 0.0670 chunk 36 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 439 ASN ** 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 = 0.3726 r_free = 0.3726 target = 0.137371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.113784 restraints weight = 4746.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116767 restraints weight = 3145.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118783 restraints weight = 2327.066| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3428 Z= 0.118 Angle : 0.566 5.698 4674 Z= 0.291 Chirality : 0.042 0.157 496 Planarity : 0.004 0.035 604 Dihedral : 4.491 24.002 474 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.51 % Allowed : 14.25 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.41), residues: 426 helix: -3.15 (0.82), residues: 21 sheet: 0.16 (0.46), residues: 151 loop : -1.47 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 106 HIS 0.002 0.001 HIS E 505 PHE 0.008 0.001 PHE E 400 TYR 0.008 0.001 TYR L 50 ARG 0.001 0.000 ARG E 454 Details of bonding type rmsd hydrogen bonds : bond 0.03071 ( 82) hydrogen bonds : angle 4.77840 ( 213) SS BOND : bond 0.00224 ( 6) SS BOND : angle 1.05169 ( 12) covalent geometry : bond 0.00285 ( 3422) covalent geometry : angle 0.56405 ( 4662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.371 Fit side-chains REVERT: E 346 ARG cc_start: 0.7526 (ttp80) cc_final: 0.7269 (ptm-80) outliers start: 9 outliers final: 9 residues processed: 65 average time/residue: 0.1239 time to fit residues: 10.3990 Evaluate side-chains 66 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 0.0040 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.0270 chunk 27 optimal weight: 0.0060 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.2266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 439 ASN ** 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 = 0.3764 r_free = 0.3764 target = 0.140777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117454 restraints weight = 4642.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120484 restraints weight = 3099.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122740 restraints weight = 2290.976| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3428 Z= 0.097 Angle : 0.535 5.546 4674 Z= 0.276 Chirality : 0.042 0.160 496 Planarity : 0.003 0.035 604 Dihedral : 4.157 20.497 474 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.23 % Allowed : 15.92 % Favored : 81.84 % 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: -1.28 (0.40), residues: 426 helix: -3.12 (0.85), residues: 21 sheet: 0.41 (0.47), residues: 141 loop : -1.43 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 106 HIS 0.001 0.000 HIS E 505 PHE 0.007 0.001 PHE E 400 TYR 0.009 0.001 TYR C 79 ARG 0.002 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.02777 ( 82) hydrogen bonds : angle 4.56970 ( 213) SS BOND : bond 0.00265 ( 6) SS BOND : angle 0.93413 ( 12) covalent geometry : bond 0.00226 ( 3422) covalent geometry : angle 0.53320 ( 4662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.405 Fit side-chains REVERT: E 346 ARG cc_start: 0.7528 (ttp80) cc_final: 0.7246 (ptm-80) REVERT: L 50 TYR cc_start: 0.6956 (p90) cc_final: 0.5865 (p90) outliers start: 8 outliers final: 8 residues processed: 70 average time/residue: 0.1537 time to fit residues: 13.5250 Evaluate side-chains 67 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113769 restraints weight = 4748.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116682 restraints weight = 3163.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118825 restraints weight = 2348.033| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3428 Z= 0.146 Angle : 0.591 5.542 4674 Z= 0.310 Chirality : 0.043 0.150 496 Planarity : 0.004 0.035 604 Dihedral : 4.378 23.717 474 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.35 % Allowed : 15.64 % Favored : 81.01 % 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: -1.37 (0.41), residues: 426 helix: -3.25 (0.80), residues: 21 sheet: 0.14 (0.45), residues: 153 loop : -1.41 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 106 HIS 0.003 0.001 HIS E 505 PHE 0.010 0.002 PHE C 107 TYR 0.008 0.001 TYR C 94 ARG 0.003 0.000 ARG E 355 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 82) hydrogen bonds : angle 4.60197 ( 213) SS BOND : bond 0.00190 ( 6) SS BOND : angle 1.13809 ( 12) covalent geometry : bond 0.00347 ( 3422) covalent geometry : angle 0.58852 ( 4662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.404 Fit side-chains REVERT: E 346 ARG cc_start: 0.7518 (ttp80) cc_final: 0.7252 (ptm-80) outliers start: 12 outliers final: 12 residues processed: 67 average time/residue: 0.1361 time to fit residues: 11.5447 Evaluate side-chains 69 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 438 SER Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 439 ASN ** 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 = 0.3695 r_free = 0.3695 target = 0.134911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.112313 restraints weight = 4705.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115066 restraints weight = 3119.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116806 restraints weight = 2320.742| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3428 Z= 0.162 Angle : 0.612 5.444 4674 Z= 0.324 Chirality : 0.043 0.148 496 Planarity : 0.004 0.038 604 Dihedral : 4.607 26.346 474 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.19 % Allowed : 15.36 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.41), residues: 426 helix: -3.21 (0.83), residues: 21 sheet: 0.11 (0.46), residues: 151 loop : -1.45 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP C 106 HIS 0.003 0.001 HIS E 505 PHE 0.011 0.002 PHE C 63 TYR 0.009 0.001 TYR C 79 ARG 0.001 0.000 ARG C 64 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 82) hydrogen bonds : angle 4.70663 ( 213) SS BOND : bond 0.00222 ( 6) SS BOND : angle 1.16351 ( 12) covalent geometry : bond 0.00383 ( 3422) covalent geometry : angle 0.61033 ( 4662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.375 Fit side-chains REVERT: C 10 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6932 (pm20) REVERT: E 346 ARG cc_start: 0.7510 (ttp80) cc_final: 0.7245 (ptm-80) REVERT: E 417 LYS cc_start: 0.8982 (ttpp) cc_final: 0.8603 (ttpp) outliers start: 15 outliers final: 13 residues processed: 67 average time/residue: 0.1356 time to fit residues: 11.4622 Evaluate side-chains 73 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 438 SER Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 439 ASN ** 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 = 0.3685 r_free = 0.3685 target = 0.134120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111183 restraints weight = 4756.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114057 restraints weight = 3116.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116232 restraints weight = 2291.841| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3428 Z= 0.166 Angle : 0.623 5.574 4674 Z= 0.328 Chirality : 0.044 0.146 496 Planarity : 0.004 0.039 604 Dihedral : 4.714 28.052 474 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.91 % Allowed : 15.36 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.41), residues: 426 helix: -3.28 (0.80), residues: 21 sheet: -0.05 (0.45), residues: 156 loop : -1.51 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 106 HIS 0.003 0.001 HIS E 505 PHE 0.013 0.002 PHE C 63 TYR 0.008 0.001 TYR C 94 ARG 0.001 0.000 ARG E 509 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 82) hydrogen bonds : angle 4.73470 ( 213) SS BOND : bond 0.00219 ( 6) SS BOND : angle 1.20237 ( 12) covalent geometry : bond 0.00394 ( 3422) covalent geometry : angle 0.62033 ( 4662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1775.07 seconds wall clock time: 31 minutes 17.99 seconds (1877.99 seconds total)