Starting phenix.real_space_refine on Fri May 9 16:18:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jrn_61761/05_2025/9jrn_61761_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jrn_61761/05_2025/9jrn_61761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jrn_61761/05_2025/9jrn_61761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jrn_61761/05_2025/9jrn_61761.map" model { file = "/net/cci-nas-00/data/ceres_data/9jrn_61761/05_2025/9jrn_61761_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jrn_61761/05_2025/9jrn_61761_neut.cif" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.055 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 11 5.16 5 C 2088 2.51 5 N 512 2.21 5 O 516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3129 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3103 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 12, 'TRANS': 373} Chain breaks: 2 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'TPP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.89, per 1000 atoms: 0.92 Number of scatterers: 3129 At special positions: 0 Unit cell: (68, 65, 75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 P 2 15.00 O 516 8.00 N 512 7.00 C 2088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 383.3 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 730 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 89.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 24 through 40 removed outlier: 4.213A pdb=" N VAL A 29 " --> pdb=" O TRP A 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 31 " --> pdb=" O HIS A 27 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.580A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 4.063A pdb=" N LEU A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 113 removed outlier: 4.338A pdb=" N VAL A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.594A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.823A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 148 through 176 removed outlier: 3.501A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 201 Processing helix chain 'A' and resid 250 through 264 removed outlier: 3.945A pdb=" N ARG A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 287 removed outlier: 3.777A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 304 through 325 removed outlier: 3.554A pdb=" N ALA A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 355 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 390 removed outlier: 3.597A pdb=" N LEU A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 395 through 419 Processing helix chain 'A' and resid 427 through 456 removed outlier: 3.746A pdb=" N GLN A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 723 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: 0.93 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 921 1.34 - 1.46: 708 1.46 - 1.57: 1566 1.57 - 1.69: 4 1.69 - 1.81: 17 Bond restraints: 3216 Sorted by residual: bond pdb=" N THR A 49 " pdb=" CA THR A 49 " ideal model delta sigma weight residual 1.461 1.487 -0.026 9.20e-03 1.18e+04 7.74e+00 bond pdb=" C THR A 49 " pdb=" N PRO A 50 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.36e-02 5.41e+03 2.13e+00 bond pdb=" CA THR A 49 " pdb=" C THR A 49 " ideal model delta sigma weight residual 1.520 1.536 -0.016 1.23e-02 6.61e+03 1.65e+00 bond pdb=" CG LEU A 426 " pdb=" CD1 LEU A 426 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.61e-01 bond pdb=" C THR A 69 " pdb=" N PRO A 70 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.48e-01 ... (remaining 3211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 4311 1.90 - 3.81: 59 3.81 - 5.71: 12 5.71 - 7.61: 0 7.61 - 9.52: 2 Bond angle restraints: 4384 Sorted by residual: angle pdb=" CA LEU A 426 " pdb=" CB LEU A 426 " pdb=" CG LEU A 426 " ideal model delta sigma weight residual 116.30 125.82 -9.52 3.50e+00 8.16e-02 7.39e+00 angle pdb=" C LEU A 28 " pdb=" N VAL A 29 " pdb=" CA VAL A 29 " ideal model delta sigma weight residual 122.63 119.80 2.83 1.19e+00 7.06e-01 5.67e+00 angle pdb=" CA LEU A 112 " pdb=" CB LEU A 112 " pdb=" CG LEU A 112 " ideal model delta sigma weight residual 116.30 124.20 -7.90 3.50e+00 8.16e-02 5.09e+00 angle pdb=" N GLY A 325 " pdb=" CA GLY A 325 " pdb=" C GLY A 325 " ideal model delta sigma weight residual 115.62 111.97 3.65 1.71e+00 3.42e-01 4.56e+00 angle pdb=" CA THR A 49 " pdb=" C THR A 49 " pdb=" O THR A 49 " ideal model delta sigma weight residual 118.73 116.81 1.92 9.80e-01 1.04e+00 3.83e+00 ... (remaining 4379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 1546 17.68 - 35.36: 228 35.36 - 53.05: 50 53.05 - 70.73: 8 70.73 - 88.41: 5 Dihedral angle restraints: 1837 sinusoidal: 701 harmonic: 1136 Sorted by residual: dihedral pdb=" CB GLU A 257 " pdb=" CG GLU A 257 " pdb=" CD GLU A 257 " pdb=" OE1 GLU A 257 " ideal model delta sinusoidal sigma weight residual 0.00 -83.60 83.60 1 3.00e+01 1.11e-03 9.48e+00 dihedral pdb=" CA GLU A 62 " pdb=" CB GLU A 62 " pdb=" CG GLU A 62 " pdb=" CD GLU A 62 " ideal model delta sinusoidal sigma weight residual 60.00 114.35 -54.35 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" N LYS A 336 " pdb=" CA LYS A 336 " pdb=" CB LYS A 336 " pdb=" CG LYS A 336 " ideal model delta sinusoidal sigma weight residual -60.00 -114.02 54.02 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 1834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 318 0.028 - 0.056: 135 0.056 - 0.084: 42 0.084 - 0.113: 11 0.113 - 0.141: 3 Chirality restraints: 509 Sorted by residual: chirality pdb=" CA THR A 69 " pdb=" N THR A 69 " pdb=" C THR A 69 " pdb=" CB THR A 69 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA ILE A 41 " pdb=" N ILE A 41 " pdb=" C ILE A 41 " pdb=" CB ILE A 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA ILE A 329 " pdb=" N ILE A 329 " pdb=" C ILE A 329 " pdb=" CB ILE A 329 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.17e-01 ... (remaining 506 not shown) Planarity restraints: 521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 103 " -0.009 2.00e-02 2.50e+03 1.11e-02 2.15e+00 pdb=" CG PHE A 103 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 103 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 103 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 103 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 103 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 103 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 145 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 146 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.53e+00 pdb=" N PRO A 82 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.018 5.00e-02 4.00e+02 ... (remaining 518 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 478 2.75 - 3.29: 3176 3.29 - 3.83: 5465 3.83 - 4.36: 6242 4.36 - 4.90: 10508 Nonbonded interactions: 25869 Sorted by model distance: nonbonded pdb=" OH TYR A 139 " pdb=" O LYS A 204 " model vdw 2.215 3.040 nonbonded pdb=" O ALA A 309 " pdb=" OG SER A 313 " model vdw 2.251 3.040 nonbonded pdb=" O TYR A 126 " pdb=" OG1 THR A 129 " model vdw 2.256 3.040 nonbonded pdb=" OG SER A 321 " pdb=" O GLN A 377 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 31 " pdb=" O LEU A 199 " model vdw 2.282 3.040 ... (remaining 25864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 13.100 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 0.036 3216 Z= 0.130 Angle : 0.594 9.517 4384 Z= 0.315 Chirality : 0.036 0.141 509 Planarity : 0.003 0.032 521 Dihedral : 17.663 88.411 1107 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.30 % Allowed : 35.24 % Favored : 64.46 % 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: 1.23 (0.42), residues: 380 helix: 1.49 (0.28), residues: 313 sheet: None (None), residues: 0 loop : -2.42 (0.64), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.002 0.001 HIS A 114 PHE 0.025 0.001 PHE A 103 TYR 0.010 0.001 TYR A 287 ARG 0.003 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.20920 ( 241) hydrogen bonds : angle 6.88908 ( 723) covalent geometry : bond 0.00268 ( 3216) covalent geometry : angle 0.59388 ( 4384) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.337 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.1194 time to fit residues: 9.9469 Evaluate side-chains 57 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 346 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.145656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.122969 restraints weight = 4988.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126566 restraints weight = 2928.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129041 restraints weight = 2070.547| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3216 Z= 0.169 Angle : 0.594 8.565 4384 Z= 0.305 Chirality : 0.039 0.155 509 Planarity : 0.004 0.036 521 Dihedral : 7.153 89.425 440 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.12 % Allowed : 28.92 % Favored : 65.96 % 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: 1.65 (0.43), residues: 380 helix: 1.67 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.92 (0.72), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.001 0.000 HIS A 27 PHE 0.036 0.002 PHE A 103 TYR 0.014 0.001 TYR A 35 ARG 0.002 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.04670 ( 241) hydrogen bonds : angle 4.40785 ( 723) covalent geometry : bond 0.00377 ( 3216) covalent geometry : angle 0.59371 ( 4384) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.315 Fit side-chains REVERT: A 77 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9153 (mm) REVERT: A 124 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8130 (tt) REVERT: A 328 LYS cc_start: 0.6168 (OUTLIER) cc_final: 0.5365 (ptmt) REVERT: A 447 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6995 (m-80) outliers start: 17 outliers final: 6 residues processed: 72 average time/residue: 0.1390 time to fit residues: 12.4699 Evaluate side-chains 66 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 447 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 0.2980 chunk 28 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.146986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124004 restraints weight = 5060.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127525 restraints weight = 3115.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129707 restraints weight = 2274.921| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3216 Z= 0.149 Angle : 0.560 8.241 4384 Z= 0.286 Chirality : 0.039 0.156 509 Planarity : 0.004 0.035 521 Dihedral : 7.051 88.996 440 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.22 % Allowed : 30.72 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.43), residues: 380 helix: 1.72 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -1.80 (0.75), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.003 0.001 HIS A 118 PHE 0.021 0.001 PHE A 103 TYR 0.011 0.001 TYR A 35 ARG 0.002 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 241) hydrogen bonds : angle 4.16677 ( 723) covalent geometry : bond 0.00331 ( 3216) covalent geometry : angle 0.56046 ( 4384) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.309 Fit side-chains REVERT: A 77 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9248 (mt) REVERT: A 124 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8101 (tt) REVERT: A 328 LYS cc_start: 0.6114 (OUTLIER) cc_final: 0.5217 (ptmt) REVERT: A 361 SER cc_start: 0.7423 (p) cc_final: 0.7099 (t) REVERT: A 434 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6766 (mp) outliers start: 14 outliers final: 6 residues processed: 73 average time/residue: 0.1166 time to fit residues: 10.9809 Evaluate side-chains 63 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 0.0170 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.146367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123935 restraints weight = 5112.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127254 restraints weight = 3075.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.129678 restraints weight = 2234.672| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3216 Z= 0.143 Angle : 0.562 8.088 4384 Z= 0.279 Chirality : 0.039 0.150 509 Planarity : 0.004 0.037 521 Dihedral : 7.041 89.052 440 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.52 % Allowed : 30.72 % Favored : 64.76 % 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: 1.92 (0.43), residues: 380 helix: 1.81 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -1.76 (0.75), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.002 0.000 HIS A 118 PHE 0.018 0.001 PHE A 103 TYR 0.012 0.001 TYR A 35 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 241) hydrogen bonds : angle 4.02070 ( 723) covalent geometry : bond 0.00319 ( 3216) covalent geometry : angle 0.56196 ( 4384) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.296 Fit side-chains REVERT: A 77 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9280 (mt) REVERT: A 124 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7991 (tt) REVERT: A 328 LYS cc_start: 0.6171 (OUTLIER) cc_final: 0.5233 (ptmt) REVERT: A 361 SER cc_start: 0.7385 (p) cc_final: 0.6963 (t) outliers start: 15 outliers final: 7 residues processed: 70 average time/residue: 0.1411 time to fit residues: 12.2590 Evaluate side-chains 63 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 419 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.145922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123494 restraints weight = 5040.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126735 restraints weight = 3078.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129131 restraints weight = 2248.832| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3216 Z= 0.141 Angle : 0.575 7.296 4384 Z= 0.284 Chirality : 0.039 0.157 509 Planarity : 0.004 0.037 521 Dihedral : 7.018 89.232 440 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 6.33 % Allowed : 30.42 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.43), residues: 380 helix: 1.85 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.86 (0.73), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.000 HIS A 118 PHE 0.023 0.001 PHE A 103 TYR 0.011 0.001 TYR A 35 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 241) hydrogen bonds : angle 3.92892 ( 723) covalent geometry : bond 0.00316 ( 3216) covalent geometry : angle 0.57462 ( 4384) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.351 Fit side-chains REVERT: A 77 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9288 (mt) REVERT: A 124 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8040 (tt) REVERT: A 136 TYR cc_start: 0.8168 (t80) cc_final: 0.7944 (t80) REVERT: A 328 LYS cc_start: 0.6260 (OUTLIER) cc_final: 0.5222 (ptmt) REVERT: A 361 SER cc_start: 0.7304 (p) cc_final: 0.7074 (t) REVERT: A 433 GLN cc_start: 0.7183 (mt0) cc_final: 0.6805 (mt0) REVERT: A 434 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6611 (mp) outliers start: 21 outliers final: 12 residues processed: 71 average time/residue: 0.1258 time to fit residues: 11.2324 Evaluate side-chains 69 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.145737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.123604 restraints weight = 5303.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.126988 restraints weight = 3149.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129437 restraints weight = 2253.499| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3216 Z= 0.135 Angle : 0.556 7.247 4384 Z= 0.279 Chirality : 0.039 0.146 509 Planarity : 0.004 0.038 521 Dihedral : 6.942 89.319 440 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 6.02 % Allowed : 30.72 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.43), residues: 380 helix: 1.90 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.89 (0.70), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.001 0.000 HIS A 118 PHE 0.019 0.001 PHE A 103 TYR 0.012 0.001 TYR A 149 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 241) hydrogen bonds : angle 3.82680 ( 723) covalent geometry : bond 0.00301 ( 3216) covalent geometry : angle 0.55576 ( 4384) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9280 (mt) REVERT: A 124 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8062 (tt) REVERT: A 136 TYR cc_start: 0.8138 (t80) cc_final: 0.7913 (t80) REVERT: A 328 LYS cc_start: 0.6335 (OUTLIER) cc_final: 0.5145 (ptmt) REVERT: A 361 SER cc_start: 0.7323 (p) cc_final: 0.6979 (t) REVERT: A 430 LYS cc_start: 0.7998 (tptp) cc_final: 0.7702 (mmmm) REVERT: A 434 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6705 (mp) outliers start: 20 outliers final: 10 residues processed: 72 average time/residue: 0.1223 time to fit residues: 11.1186 Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.146215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124252 restraints weight = 5146.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127324 restraints weight = 3112.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129810 restraints weight = 2286.224| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3216 Z= 0.129 Angle : 0.559 6.940 4384 Z= 0.275 Chirality : 0.039 0.159 509 Planarity : 0.004 0.040 521 Dihedral : 6.878 89.623 440 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.52 % Allowed : 30.72 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.43), residues: 380 helix: 1.98 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.78 (0.72), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.001 0.000 HIS A 27 PHE 0.023 0.002 PHE A 351 TYR 0.011 0.001 TYR A 149 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 241) hydrogen bonds : angle 3.77519 ( 723) covalent geometry : bond 0.00287 ( 3216) covalent geometry : angle 0.55854 ( 4384) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.304 Fit side-chains REVERT: A 77 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9257 (mt) REVERT: A 89 TYR cc_start: 0.6719 (t80) cc_final: 0.6452 (t80) REVERT: A 124 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8085 (tt) REVERT: A 328 LYS cc_start: 0.6214 (OUTLIER) cc_final: 0.4880 (ptmt) REVERT: A 361 SER cc_start: 0.7395 (p) cc_final: 0.7175 (t) REVERT: A 385 PHE cc_start: 0.8430 (t80) cc_final: 0.8196 (t80) REVERT: A 426 LEU cc_start: 0.7507 (mp) cc_final: 0.7299 (mp) REVERT: A 434 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6766 (mp) outliers start: 15 outliers final: 8 residues processed: 71 average time/residue: 0.1184 time to fit residues: 10.9529 Evaluate side-chains 67 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.150201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128245 restraints weight = 4939.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.132021 restraints weight = 2842.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134297 restraints weight = 1981.154| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3216 Z= 0.161 Angle : 0.583 6.779 4384 Z= 0.291 Chirality : 0.040 0.153 509 Planarity : 0.004 0.038 521 Dihedral : 6.860 89.369 440 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.42 % Allowed : 31.93 % Favored : 62.65 % 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: 2.08 (0.43), residues: 380 helix: 1.90 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.42 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 107 HIS 0.002 0.001 HIS A 27 PHE 0.021 0.002 PHE A 103 TYR 0.021 0.001 TYR A 136 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 241) hydrogen bonds : angle 3.81022 ( 723) covalent geometry : bond 0.00371 ( 3216) covalent geometry : angle 0.58335 ( 4384) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.311 Fit side-chains REVERT: A 77 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9308 (mt) REVERT: A 124 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8192 (tt) REVERT: A 361 SER cc_start: 0.7393 (p) cc_final: 0.7088 (t) REVERT: A 426 LEU cc_start: 0.7464 (mp) cc_final: 0.7256 (mp) REVERT: A 434 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6783 (mp) REVERT: A 447 PHE cc_start: 0.7126 (t80) cc_final: 0.6925 (t80) outliers start: 18 outliers final: 10 residues processed: 68 average time/residue: 0.1123 time to fit residues: 9.8539 Evaluate side-chains 66 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.152525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130826 restraints weight = 4989.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134632 restraints weight = 2868.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.136976 restraints weight = 1991.960| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3216 Z= 0.128 Angle : 0.575 6.791 4384 Z= 0.283 Chirality : 0.039 0.165 509 Planarity : 0.004 0.040 521 Dihedral : 6.756 89.040 440 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.61 % Allowed : 34.04 % Favored : 62.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.43), residues: 380 helix: 1.97 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.62 (0.74), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.001 0.000 HIS A 27 PHE 0.022 0.001 PHE A 351 TYR 0.014 0.001 TYR A 136 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 241) hydrogen bonds : angle 3.73034 ( 723) covalent geometry : bond 0.00282 ( 3216) covalent geometry : angle 0.57540 ( 4384) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.350 Fit side-chains REVERT: A 124 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8181 (tt) REVERT: A 361 SER cc_start: 0.7389 (p) cc_final: 0.7134 (t) REVERT: A 385 PHE cc_start: 0.8414 (t80) cc_final: 0.8175 (t80) REVERT: A 426 LEU cc_start: 0.7436 (mp) cc_final: 0.7218 (mp) REVERT: A 434 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6919 (mp) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.1154 time to fit residues: 9.8559 Evaluate side-chains 63 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 32 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.152068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130630 restraints weight = 4829.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134342 restraints weight = 2792.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136776 restraints weight = 1958.963| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3216 Z= 0.134 Angle : 0.574 6.590 4384 Z= 0.282 Chirality : 0.039 0.164 509 Planarity : 0.004 0.039 521 Dihedral : 6.680 88.373 440 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.31 % Allowed : 34.34 % Favored : 62.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.43), residues: 380 helix: 2.01 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.69 (0.74), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 107 HIS 0.002 0.001 HIS A 118 PHE 0.019 0.001 PHE A 103 TYR 0.015 0.001 TYR A 136 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 241) hydrogen bonds : angle 3.71076 ( 723) covalent geometry : bond 0.00301 ( 3216) covalent geometry : angle 0.57355 ( 4384) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.346 Fit side-chains REVERT: A 124 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8172 (tt) REVERT: A 361 SER cc_start: 0.7422 (p) cc_final: 0.7140 (t) REVERT: A 385 PHE cc_start: 0.8432 (t80) cc_final: 0.8191 (t80) REVERT: A 434 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6738 (mp) outliers start: 11 outliers final: 8 residues processed: 62 average time/residue: 0.1100 time to fit residues: 9.0435 Evaluate side-chains 63 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 0.0670 chunk 24 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 0.0770 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.153214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.131715 restraints weight = 4995.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.135522 restraints weight = 2855.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.138009 restraints weight = 1981.556| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3216 Z= 0.122 Angle : 0.590 12.592 4384 Z= 0.281 Chirality : 0.039 0.163 509 Planarity : 0.004 0.038 521 Dihedral : 6.622 88.146 440 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.01 % Allowed : 34.94 % Favored : 62.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.43), residues: 380 helix: 2.06 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -1.73 (0.72), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.001 0.000 HIS A 118 PHE 0.023 0.001 PHE A 351 TYR 0.016 0.001 TYR A 136 ARG 0.002 0.000 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 241) hydrogen bonds : angle 3.69187 ( 723) covalent geometry : bond 0.00269 ( 3216) covalent geometry : angle 0.58958 ( 4384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1284.17 seconds wall clock time: 23 minutes 13.58 seconds (1393.58 seconds total)