Starting phenix.real_space_refine on Wed Jun 4 14:23:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrl_32732/06_2025/7wrl_32732.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrl_32732/06_2025/7wrl_32732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wrl_32732/06_2025/7wrl_32732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrl_32732/06_2025/7wrl_32732.map" model { file = "/net/cci-nas-00/data/ceres_data/7wrl_32732/06_2025/7wrl_32732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrl_32732/06_2025/7wrl_32732.cif" } resolution = 3.51 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= 0.043 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 2052 2.51 5 N 548 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3251 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 971 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "B" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 776 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "R" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1504 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Time building chain proxies: 2.76, per 1000 atoms: 0.85 Number of scatterers: 3251 At special positions: 0 Unit cell: (63.72, 82.08, 76.68, 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 636 8.00 N 548 7.00 C 2052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " 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: 0.68 Conformation dependent library (CDL) restraints added in 367.4 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 11 sheets defined 5.0% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.969A pdb=" N GLN A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.608A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 390 removed outlier: 3.578A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN R 388 " --> pdb=" O THR R 385 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP R 389 " --> pdb=" O LYS R 386 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU R 390 " --> pdb=" O LEU R 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 384 through 390' Processing helix chain 'R' and resid 498 through 502 removed outlier: 3.785A pdb=" N TYR R 501 " --> pdb=" O ARG R 498 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY R 502 " --> pdb=" O PRO R 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 498 through 502' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 39 removed outlier: 6.876A pdb=" N SER A 34 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ARG A 50 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 72 through 73 removed outlier: 3.508A pdb=" N ASP A 73 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 78 " --> pdb=" O ASP A 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA6, first strand: chain 'A' and resid 97 through 101 removed outlier: 4.703A pdb=" N VAL A 119 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL A 100 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N MET A 117 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.831A pdb=" N SER B 65 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 50 removed outlier: 6.537A pdb=" N TRP B 37 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 356 through 358 Processing sheet with id=AB1, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.995A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'R' and resid 452 through 454 51 hydrogen bonds defined for protein. 117 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: 0.75 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: 1017 1.34 - 1.46: 739 1.46 - 1.57: 1558 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3332 Sorted by residual: bond pdb=" C ASP A 109 " pdb=" N PHE A 110 " ideal model delta sigma weight residual 1.334 1.305 0.030 1.49e-02 4.50e+03 3.93e+00 bond pdb=" CB CYS B 90 " pdb=" SG CYS B 90 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.39e+00 bond pdb=" C LYS A 13 " pdb=" N PRO A 14 " ideal model delta sigma weight residual 1.330 1.349 -0.019 1.25e-02 6.40e+03 2.35e+00 bond pdb=" N ALA R 411 " pdb=" CA ALA R 411 " ideal model delta sigma weight residual 1.457 1.436 0.021 1.41e-02 5.03e+03 2.13e+00 bond pdb=" C ALA R 372 " pdb=" N PRO R 373 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.04e+00 ... (remaining 3327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 4176 1.79 - 3.58: 285 3.58 - 5.37: 55 5.37 - 7.16: 9 7.16 - 8.95: 4 Bond angle restraints: 4529 Sorted by residual: angle pdb=" N VAL R 483 " pdb=" CA VAL R 483 " pdb=" C VAL R 483 " ideal model delta sigma weight residual 106.21 110.82 -4.61 1.07e+00 8.73e-01 1.86e+01 angle pdb=" C GLY R 485 " pdb=" N PHE R 486 " pdb=" CA PHE R 486 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" N VAL R 367 " pdb=" CA VAL R 367 " pdb=" C VAL R 367 " ideal model delta sigma weight residual 112.29 108.61 3.68 9.40e-01 1.13e+00 1.53e+01 angle pdb=" OG1 THR B 94 " pdb=" CB THR B 94 " pdb=" CG2 THR B 94 " ideal model delta sigma weight residual 109.30 102.03 7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" C TYR B 51 " pdb=" N ASP B 52 " pdb=" CA ASP B 52 " ideal model delta sigma weight residual 121.71 116.85 4.86 1.39e+00 5.18e-01 1.22e+01 ... (remaining 4524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 1709 17.40 - 34.79: 196 34.79 - 52.19: 33 52.19 - 69.59: 5 69.59 - 86.98: 1 Dihedral angle restraints: 1944 sinusoidal: 734 harmonic: 1210 Sorted by residual: dihedral pdb=" CA LYS A 13 " pdb=" C LYS A 13 " pdb=" N PRO A 14 " pdb=" CA PRO A 14 " ideal model delta harmonic sigma weight residual -180.00 -145.72 -34.28 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" CA TYR A 60 " pdb=" C TYR A 60 " pdb=" N ALA A 61 " pdb=" CA ALA A 61 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ARG R 466 " pdb=" C ARG R 466 " pdb=" N ASP R 467 " pdb=" CA ASP R 467 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 1941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 307 0.047 - 0.094: 120 0.094 - 0.141: 43 0.141 - 0.188: 11 0.188 - 0.235: 4 Chirality restraints: 485 Sorted by residual: chirality pdb=" CB ILE A 51 " pdb=" CA ILE A 51 " pdb=" CG1 ILE A 51 " pdb=" CG2 ILE A 51 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA TYR B 51 " pdb=" N TYR B 51 " pdb=" C TYR B 51 " pdb=" CB TYR B 51 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB VAL R 483 " pdb=" CA VAL R 483 " pdb=" CG1 VAL R 483 " pdb=" CG2 VAL R 483 " both_signs ideal model delta sigma weight residual False -2.63 -2.85 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 482 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS R 462 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO R 463 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO R 463 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 463 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 338 " -0.014 2.00e-02 2.50e+03 1.75e-02 5.37e+00 pdb=" CG PHE R 338 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE R 338 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE R 338 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE R 338 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 338 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE R 338 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 56 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO B 57 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 57 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 57 " 0.031 5.00e-02 4.00e+02 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 986 2.81 - 3.33: 2686 3.33 - 3.86: 5412 3.86 - 4.38: 6037 4.38 - 4.90: 10870 Nonbonded interactions: 25991 Sorted by model distance: nonbonded pdb=" OG1 THR R 415 " pdb=" OD2 ASP R 420 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR B 32 " pdb=" OD2 ASP R 405 " model vdw 2.312 3.040 nonbonded pdb=" ND2 ASN B 54 " pdb=" O GLY B 66 " model vdw 2.322 3.120 nonbonded pdb=" O SER A 25 " pdb=" OG SER A 25 " model vdw 2.327 3.040 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.327 3.040 ... (remaining 25986 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: 3.570 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: 0.030 Set scattering table: 0.030 Process input model: 12.640 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.006 0.054 3335 Z= 0.273 Angle : 1.031 8.952 4535 Z= 0.594 Chirality : 0.060 0.235 485 Planarity : 0.008 0.075 586 Dihedral : 14.713 86.983 1171 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -4.19 (0.37), residues: 411 helix: -4.93 (0.34), residues: 27 sheet: -2.41 (0.46), residues: 118 loop : -2.86 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 47 HIS 0.002 0.001 HIS B 41 PHE 0.040 0.003 PHE R 338 TYR 0.032 0.003 TYR B 51 ARG 0.023 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.24310 ( 51) hydrogen bonds : angle 10.83828 ( 117) SS BOND : bond 0.00123 ( 3) SS BOND : angle 0.52933 ( 6) covalent geometry : bond 0.00591 ( 3332) covalent geometry : angle 1.03124 ( 4529) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.294 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1781 time to fit residues: 14.6205 Evaluate side-chains 50 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.0270 chunk 12 optimal weight: 0.0980 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 54 ASN ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.143789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.115611 restraints weight = 5159.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119188 restraints weight = 3174.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.121739 restraints weight = 2340.737| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 3335 Z= 0.120 Angle : 0.607 5.627 4535 Z= 0.332 Chirality : 0.044 0.158 485 Planarity : 0.006 0.063 586 Dihedral : 6.262 25.335 466 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 1.13 % Allowed : 10.14 % Favored : 88.73 % 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: -3.78 (0.38), residues: 411 helix: -4.43 (0.58), residues: 27 sheet: -1.58 (0.47), residues: 116 loop : -2.91 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 120 HIS 0.002 0.001 HIS B 41 PHE 0.019 0.001 PHE R 338 TYR 0.019 0.002 TYR B 51 ARG 0.002 0.000 ARG R 457 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 51) hydrogen bonds : angle 7.97135 ( 117) SS BOND : bond 0.00053 ( 3) SS BOND : angle 0.67071 ( 6) covalent geometry : bond 0.00303 ( 3332) covalent geometry : angle 0.60700 ( 4529) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.394 Fit side-chains REVERT: R 405 ASP cc_start: 0.8597 (p0) cc_final: 0.8303 (p0) outliers start: 4 outliers final: 3 residues processed: 71 average time/residue: 0.1709 time to fit residues: 14.6878 Evaluate side-chains 62 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 53 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 5 optimal weight: 0.0050 chunk 22 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** R 487 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 = 0.3816 r_free = 0.3816 target = 0.137952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109612 restraints weight = 5230.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112866 restraints weight = 3409.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.115130 restraints weight = 2603.183| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3335 Z= 0.269 Angle : 0.699 6.106 4535 Z= 0.386 Chirality : 0.048 0.191 485 Planarity : 0.006 0.058 586 Dihedral : 6.308 24.493 466 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.87 % Favored : 86.13 % Rotamer: Outliers : 3.10 % Allowed : 14.37 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.37), residues: 411 helix: -4.51 (0.56), residues: 27 sheet: -1.77 (0.47), residues: 116 loop : -2.94 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 120 HIS 0.001 0.000 HIS R 505 PHE 0.019 0.002 PHE B 101 TYR 0.023 0.002 TYR B 51 ARG 0.003 0.000 ARG R 454 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 51) hydrogen bonds : angle 7.87423 ( 117) SS BOND : bond 0.00132 ( 3) SS BOND : angle 1.22729 ( 6) covalent geometry : bond 0.00611 ( 3332) covalent geometry : angle 0.69802 ( 4529) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: B 44 LYS cc_start: 0.7248 (mptt) cc_final: 0.6258 (ptmm) REVERT: B 81 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7946 (tm-30) outliers start: 11 outliers final: 9 residues processed: 59 average time/residue: 0.1590 time to fit residues: 11.5592 Evaluate side-chains 64 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 393 THR Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain R residue 501 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** R 487 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 = 0.3847 r_free = 0.3847 target = 0.140810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112675 restraints weight = 5316.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.116171 restraints weight = 3336.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.118523 restraints weight = 2481.181| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3335 Z= 0.165 Angle : 0.608 5.955 4535 Z= 0.334 Chirality : 0.045 0.163 485 Planarity : 0.005 0.058 586 Dihedral : 5.772 21.560 466 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.90 % Favored : 87.10 % Rotamer: Outliers : 2.82 % Allowed : 16.06 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.37), residues: 411 helix: -4.46 (0.58), residues: 27 sheet: -1.69 (0.45), residues: 124 loop : -2.97 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 120 HIS 0.000 0.000 HIS B 41 PHE 0.021 0.002 PHE R 490 TYR 0.022 0.002 TYR B 51 ARG 0.002 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.02906 ( 51) hydrogen bonds : angle 7.43945 ( 117) SS BOND : bond 0.00267 ( 3) SS BOND : angle 1.50001 ( 6) covalent geometry : bond 0.00385 ( 3332) covalent geometry : angle 0.60614 ( 4529) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.384 Fit side-chains REVERT: B 81 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7821 (tm-30) outliers start: 10 outliers final: 8 residues processed: 63 average time/residue: 0.1445 time to fit residues: 11.4580 Evaluate side-chains 62 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 393 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 0.0020 chunk 16 optimal weight: 0.1980 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** R 487 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 = 0.3862 r_free = 0.3862 target = 0.142704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.114007 restraints weight = 5150.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.117670 restraints weight = 3177.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.120144 restraints weight = 2353.081| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3335 Z= 0.111 Angle : 0.578 6.215 4535 Z= 0.312 Chirality : 0.043 0.151 485 Planarity : 0.005 0.059 586 Dihedral : 5.435 23.084 466 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 2.25 % Allowed : 19.15 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.38), residues: 411 helix: -4.33 (0.63), residues: 27 sheet: -1.41 (0.47), residues: 122 loop : -2.86 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 47 HIS 0.000 0.000 HIS B 41 PHE 0.014 0.001 PHE R 490 TYR 0.020 0.001 TYR B 51 ARG 0.002 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.02508 ( 51) hydrogen bonds : angle 7.09424 ( 117) SS BOND : bond 0.00145 ( 3) SS BOND : angle 0.80097 ( 6) covalent geometry : bond 0.00261 ( 3332) covalent geometry : angle 0.57742 ( 4529) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.357 Fit side-chains REVERT: A 84 ARG cc_start: 0.7690 (mtm110) cc_final: 0.7418 (mtm110) REVERT: B 81 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7724 (tm-30) outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 0.1665 time to fit residues: 13.4819 Evaluate side-chains 58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 374 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 2 optimal weight: 0.0470 chunk 14 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** R 487 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 = 0.3837 r_free = 0.3837 target = 0.140484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111123 restraints weight = 5392.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.114646 restraints weight = 3394.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117048 restraints weight = 2539.429| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3335 Z= 0.171 Angle : 0.604 5.944 4535 Z= 0.328 Chirality : 0.044 0.161 485 Planarity : 0.005 0.058 586 Dihedral : 5.402 20.560 466 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer: Outliers : 2.54 % Allowed : 20.56 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.38), residues: 411 helix: -4.33 (0.65), residues: 27 sheet: -1.52 (0.47), residues: 124 loop : -2.96 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 120 HIS 0.000 0.000 HIS B 41 PHE 0.014 0.002 PHE R 490 TYR 0.021 0.002 TYR B 51 ARG 0.003 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.02778 ( 51) hydrogen bonds : angle 7.02255 ( 117) SS BOND : bond 0.00249 ( 3) SS BOND : angle 1.31017 ( 6) covalent geometry : bond 0.00397 ( 3332) covalent geometry : angle 0.60278 ( 4529) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.366 Fit side-chains REVERT: A 84 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7493 (mtm110) REVERT: B 81 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7739 (tm-30) outliers start: 9 outliers final: 9 residues processed: 57 average time/residue: 0.1333 time to fit residues: 9.7087 Evaluate side-chains 58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 374 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 487 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 = 0.3846 r_free = 0.3846 target = 0.141285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112504 restraints weight = 5147.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.116041 restraints weight = 3227.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118367 restraints weight = 2407.472| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3335 Z= 0.140 Angle : 0.589 6.488 4535 Z= 0.318 Chirality : 0.044 0.154 485 Planarity : 0.004 0.057 586 Dihedral : 5.259 20.895 466 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 3.66 % Allowed : 20.85 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.39), residues: 411 helix: -4.32 (0.66), residues: 27 sheet: -1.31 (0.49), residues: 120 loop : -2.75 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.000 0.000 HIS B 41 PHE 0.013 0.001 PHE R 490 TYR 0.020 0.001 TYR B 51 ARG 0.002 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.02618 ( 51) hydrogen bonds : angle 6.81223 ( 117) SS BOND : bond 0.00083 ( 3) SS BOND : angle 1.28826 ( 6) covalent geometry : bond 0.00326 ( 3332) covalent geometry : angle 0.58736 ( 4529) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.6910 (ttm170) REVERT: A 84 ARG cc_start: 0.7768 (mtm110) cc_final: 0.7506 (mtm110) REVERT: B 81 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7731 (tm-30) REVERT: R 386 LYS cc_start: 0.8609 (ptpp) cc_final: 0.8275 (ptpp) outliers start: 13 outliers final: 10 residues processed: 66 average time/residue: 0.1602 time to fit residues: 12.9729 Evaluate side-chains 64 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 374 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 16 optimal weight: 0.0470 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 487 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 = 0.3880 r_free = 0.3880 target = 0.144210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115675 restraints weight = 5137.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.119316 restraints weight = 3211.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.121685 restraints weight = 2390.998| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3335 Z= 0.109 Angle : 0.570 6.828 4535 Z= 0.304 Chirality : 0.043 0.151 485 Planarity : 0.004 0.056 586 Dihedral : 4.988 21.226 466 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 3.38 % Allowed : 21.69 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.39), residues: 411 helix: -4.56 (0.71), residues: 21 sheet: -1.13 (0.49), residues: 120 loop : -2.69 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 47 HIS 0.000 0.000 HIS B 41 PHE 0.011 0.001 PHE R 490 TYR 0.019 0.001 TYR B 51 ARG 0.001 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.02439 ( 51) hydrogen bonds : angle 6.59885 ( 117) SS BOND : bond 0.00081 ( 3) SS BOND : angle 1.42668 ( 6) covalent geometry : bond 0.00267 ( 3332) covalent geometry : angle 0.56818 ( 4529) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: R 444 LYS cc_start: 0.6303 (tppt) cc_final: 0.5490 (pttt) outliers start: 12 outliers final: 9 residues processed: 68 average time/residue: 0.1357 time to fit residues: 11.6345 Evaluate side-chains 57 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 374 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN ** R 487 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 = 0.3877 r_free = 0.3877 target = 0.143741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115378 restraints weight = 5174.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.118975 restraints weight = 3166.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.121514 restraints weight = 2336.386| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3335 Z= 0.126 Angle : 0.592 7.656 4535 Z= 0.318 Chirality : 0.043 0.149 485 Planarity : 0.004 0.056 586 Dihedral : 5.006 20.955 466 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 3.38 % Allowed : 21.97 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.39), residues: 411 helix: -4.18 (0.74), residues: 27 sheet: -1.09 (0.49), residues: 120 loop : -2.74 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.001 0.000 HIS B 41 PHE 0.011 0.001 PHE R 490 TYR 0.019 0.001 TYR B 51 ARG 0.002 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.02453 ( 51) hydrogen bonds : angle 6.55105 ( 117) SS BOND : bond 0.00041 ( 3) SS BOND : angle 1.56145 ( 6) covalent geometry : bond 0.00302 ( 3332) covalent geometry : angle 0.58965 ( 4529) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7654 (mtm110) cc_final: 0.7266 (mtm110) REVERT: A 89 GLU cc_start: 0.5960 (pp20) cc_final: 0.5358 (mm-30) REVERT: R 444 LYS cc_start: 0.6161 (tppt) cc_final: 0.5417 (pttt) outliers start: 12 outliers final: 11 residues processed: 62 average time/residue: 0.1550 time to fit residues: 11.8738 Evaluate side-chains 60 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 5 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN ** R 487 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 = 0.3859 r_free = 0.3859 target = 0.142433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113469 restraints weight = 5217.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.116977 restraints weight = 3300.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.119327 restraints weight = 2473.927| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3335 Z= 0.160 Angle : 0.638 7.651 4535 Z= 0.342 Chirality : 0.045 0.152 485 Planarity : 0.004 0.054 586 Dihedral : 5.069 20.578 466 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 3.10 % Allowed : 22.82 % Favored : 74.08 % 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: -3.46 (0.39), residues: 411 helix: -4.22 (0.71), residues: 27 sheet: -1.25 (0.48), residues: 120 loop : -2.75 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 120 HIS 0.001 0.001 HIS B 41 PHE 0.012 0.001 PHE B 101 TYR 0.020 0.002 TYR B 51 ARG 0.002 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.02675 ( 51) hydrogen bonds : angle 6.70739 ( 117) SS BOND : bond 0.00913 ( 3) SS BOND : angle 1.77516 ( 6) covalent geometry : bond 0.00376 ( 3332) covalent geometry : angle 0.63512 ( 4529) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7665 (mtm110) cc_final: 0.7302 (mtm110) outliers start: 11 outliers final: 11 residues processed: 61 average time/residue: 0.1533 time to fit residues: 11.7066 Evaluate side-chains 63 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 374 PHE Chi-restraints excluded: chain R residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.0030 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 487 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 = 0.3860 r_free = 0.3860 target = 0.142567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.113873 restraints weight = 5169.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117362 restraints weight = 3257.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.119789 restraints weight = 2444.400| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3335 Z= 0.150 Angle : 0.622 7.721 4535 Z= 0.335 Chirality : 0.044 0.153 485 Planarity : 0.004 0.054 586 Dihedral : 5.066 20.566 466 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 3.10 % Allowed : 23.10 % Favored : 73.80 % 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: -3.43 (0.38), residues: 411 helix: -4.18 (0.72), residues: 27 sheet: -1.25 (0.48), residues: 120 loop : -2.72 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 120 HIS 0.002 0.001 HIS B 41 PHE 0.014 0.002 PHE R 338 TYR 0.020 0.002 TYR B 51 ARG 0.002 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.02721 ( 51) hydrogen bonds : angle 6.65481 ( 117) SS BOND : bond 0.00673 ( 3) SS BOND : angle 1.64075 ( 6) covalent geometry : bond 0.00355 ( 3332) covalent geometry : angle 0.61974 ( 4529) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1715.88 seconds wall clock time: 30 minutes 21.67 seconds (1821.67 seconds total)