Starting phenix.real_space_refine on Wed Mar 5 17:34:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jrn_61761/03_2025/9jrn_61761_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jrn_61761/03_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_61761/03_2025/9jrn_61761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jrn_61761/03_2025/9jrn_61761.map" model { file = "/net/cci-nas-00/data/ceres_data/9jrn_61761/03_2025/9jrn_61761_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jrn_61761/03_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-5624/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: 2.72, per 1000 atoms: 0.87 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: 0.84 Conformation dependent library (CDL) restraints added in 382.0 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: 0.30 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: 0.84 Time building geometry restraints manager: 0.98 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.770 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.470 ------------------------------------------------------------------------------- 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= 0.178 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 *********************** 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 : 0.352 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.1217 time to fit residues: 10.2171 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 : 0.373 ------------------------------------------------------------------------------- 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 = 0.122970 restraints weight = 4988.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126566 restraints weight = 2928.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129007 restraints weight = 2070.668| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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= 0.250 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 *********************** 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 : 0.331 Fit side-chains REVERT: A 77 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9156 (mm) REVERT: A 124 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8135 (tt) REVERT: A 328 LYS cc_start: 0.6170 (OUTLIER) cc_final: 0.5373 (ptmt) REVERT: A 447 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6985 (m-80) outliers start: 17 outliers final: 6 residues processed: 72 average time/residue: 0.1397 time to fit residues: 12.4501 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 : 0.356 ------------------------------------------------------------------------------- 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: 0.7980 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 28 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.145642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123561 restraints weight = 4991.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.126926 restraints weight = 3007.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.129325 restraints weight = 2163.780| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2154 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= 0.222 Angle : 0.565 7.946 4384 Z= 0.290 Chirality : 0.039 0.157 509 Planarity : 0.004 0.035 521 Dihedral : 7.063 89.081 440 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.82 % Allowed : 30.12 % 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 : -1.83 (0.74), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.001 HIS A 118 PHE 0.023 0.001 PHE A 103 TYR 0.012 0.001 TYR A 35 ARG 0.002 0.000 ARG A 357 *********************** 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 79 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.356 Fit side-chains REVERT: A 77 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9253 (mt) REVERT: A 124 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8090 (tt) REVERT: A 328 LYS cc_start: 0.6048 (OUTLIER) cc_final: 0.5189 (ptmt) REVERT: A 361 SER cc_start: 0.7381 (p) cc_final: 0.7015 (t) REVERT: A 434 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6900 (mt) outliers start: 16 outliers final: 8 residues processed: 77 average time/residue: 0.1148 time to fit residues: 11.2322 Evaluate side-chains 66 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 419 SER 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: 0.9980 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.0010 chunk 2 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.146699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124371 restraints weight = 5121.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127856 restraints weight = 3052.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130044 restraints weight = 2184.429| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3216 Z= 0.198 Angle : 0.564 8.075 4384 Z= 0.280 Chirality : 0.039 0.150 509 Planarity : 0.004 0.037 521 Dihedral : 7.040 88.999 440 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.92 % Allowed : 31.02 % 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: 1.91 (0.43), residues: 380 helix: 1.81 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -1.78 (0.75), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.002 0.000 HIS A 118 PHE 0.015 0.001 PHE A 103 TYR 0.011 0.001 TYR A 35 ARG 0.003 0.000 ARG A 42 *********************** 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 71 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.357 Fit side-chains REVERT: A 77 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9269 (mt) REVERT: A 122 MET cc_start: 0.8415 (ppp) cc_final: 0.8043 (ppp) REVERT: A 124 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7970 (tt) REVERT: A 328 LYS cc_start: 0.6134 (OUTLIER) cc_final: 0.5213 (ptmt) REVERT: A 361 SER cc_start: 0.7390 (p) cc_final: 0.6989 (t) outliers start: 13 outliers final: 7 residues processed: 68 average time/residue: 0.1379 time to fit residues: 11.7475 Evaluate side-chains 62 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.146036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123387 restraints weight = 5064.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.126845 restraints weight = 3080.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.128547 restraints weight = 2233.654| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3216 Z= 0.220 Angle : 0.582 7.465 4384 Z= 0.288 Chirality : 0.039 0.150 509 Planarity : 0.004 0.037 521 Dihedral : 7.041 89.256 440 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.33 % Allowed : 30.72 % Favored : 62.95 % 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: 1.86 (0.43), residues: 380 helix: 1.79 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.81 (0.74), residues: 60 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 0.020 0.001 PHE A 103 TYR 0.012 0.001 TYR A 35 ARG 0.002 0.000 ARG A 42 *********************** 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 75 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9298 (mt) REVERT: A 124 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8060 (tt) REVERT: A 136 TYR cc_start: 0.8185 (t80) cc_final: 0.7961 (t80) REVERT: A 328 LYS cc_start: 0.6217 (OUTLIER) cc_final: 0.5201 (ptmt) REVERT: A 361 SER cc_start: 0.7360 (p) cc_final: 0.7084 (t) REVERT: A 433 GLN cc_start: 0.7126 (mt0) cc_final: 0.6737 (mt0) REVERT: A 434 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6626 (mp) outliers start: 21 outliers final: 11 residues processed: 71 average time/residue: 0.1383 time to fit residues: 12.3906 Evaluate side-chains 67 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.144021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121876 restraints weight = 5274.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125268 restraints weight = 3136.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.127719 restraints weight = 2227.965| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3216 Z= 0.233 Angle : 0.572 7.152 4384 Z= 0.289 Chirality : 0.039 0.149 509 Planarity : 0.004 0.037 521 Dihedral : 6.992 89.486 440 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.72 % Allowed : 31.02 % 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: 1.90 (0.43), residues: 380 helix: 1.84 (0.28), residues: 319 sheet: None (None), residues: 0 loop : -1.87 (0.72), residues: 61 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 0.013 0.001 TYR A 149 ARG 0.003 0.000 ARG A 42 *********************** 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 74 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9311 (mt) REVERT: A 124 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8098 (tt) REVERT: A 136 TYR cc_start: 0.8172 (t80) cc_final: 0.7936 (t80) REVERT: A 328 LYS cc_start: 0.6336 (OUTLIER) cc_final: 0.5103 (ptmt) REVERT: A 361 SER cc_start: 0.7332 (p) cc_final: 0.6983 (t) REVERT: A 430 LYS cc_start: 0.8035 (tptp) cc_final: 0.7731 (mmmm) REVERT: A 434 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6680 (mp) outliers start: 19 outliers final: 12 residues processed: 69 average time/residue: 0.1316 time to fit residues: 11.5394 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 : 0.349 ------------------------------------------------------------------------------- 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 339 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 431 GLN 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: 3.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.144185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122065 restraints weight = 5113.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125359 restraints weight = 3102.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127683 restraints weight = 2244.577| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3066 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= 0.221 Angle : 0.569 7.000 4384 Z= 0.286 Chirality : 0.039 0.162 509 Planarity : 0.004 0.037 521 Dihedral : 6.973 89.725 440 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.63 % Allowed : 29.52 % Favored : 63.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.43), residues: 380 helix: 1.88 (0.28), residues: 319 sheet: None (None), residues: 0 loop : -1.78 (0.72), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 107 HIS 0.001 0.000 HIS A 27 PHE 0.021 0.001 PHE A 103 TYR 0.012 0.001 TYR A 35 ARG 0.002 0.000 ARG A 42 *********************** 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 75 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.325 Fit side-chains REVERT: A 77 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9306 (mt) REVERT: A 89 TYR cc_start: 0.6890 (t80) cc_final: 0.6533 (t80) REVERT: A 119 MET cc_start: 0.8211 (mmt) cc_final: 0.7939 (mmt) REVERT: A 124 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8101 (tt) REVERT: A 328 LYS cc_start: 0.6365 (OUTLIER) cc_final: 0.5126 (ptmt) REVERT: A 361 SER cc_start: 0.7399 (p) cc_final: 0.7156 (t) REVERT: A 431 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7155 (mm-40) REVERT: A 434 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6703 (mp) outliers start: 22 outliers final: 12 residues processed: 69 average time/residue: 0.1226 time to fit residues: 10.8278 Evaluate side-chains 69 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 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 431 GLN 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: 0.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.144995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123012 restraints weight = 5187.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126501 restraints weight = 3106.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.128650 restraints weight = 2214.979| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3216 Z= 0.191 Angle : 0.582 11.642 4384 Z= 0.283 Chirality : 0.039 0.161 509 Planarity : 0.004 0.037 521 Dihedral : 6.916 89.832 440 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.12 % Allowed : 31.63 % 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: 2.08 (0.43), residues: 380 helix: 1.94 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.67 (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 0.017 0.001 PHE A 103 TYR 0.013 0.001 TYR A 136 ARG 0.002 0.000 ARG A 42 *********************** 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: 17 poor density : 56 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9286 (mt) REVERT: A 89 TYR cc_start: 0.6795 (t80) cc_final: 0.6466 (t80) REVERT: A 119 MET cc_start: 0.8237 (mmt) cc_final: 0.7869 (mmt) REVERT: A 124 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8090 (tt) REVERT: A 328 LYS cc_start: 0.6386 (OUTLIER) cc_final: 0.5116 (ptmt) REVERT: A 361 SER cc_start: 0.7408 (p) cc_final: 0.7145 (t) REVERT: A 434 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6662 (mp) outliers start: 17 outliers final: 12 residues processed: 69 average time/residue: 0.1189 time to fit residues: 10.5340 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 : 0.329 ------------------------------------------------------------------------------- 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 177 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 291 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 431 GLN 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: 1.9990 chunk 21 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.0870 chunk 3 optimal weight: 0.0050 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 overall best weight: 0.3772 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.145998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124087 restraints weight = 5240.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127460 restraints weight = 3116.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129869 restraints weight = 2227.026| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3216 Z= 0.171 Angle : 0.567 11.765 4384 Z= 0.275 Chirality : 0.039 0.161 509 Planarity : 0.004 0.039 521 Dihedral : 6.861 89.868 440 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 : 4.52 % Allowed : 32.53 % Favored : 62.95 % 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: 1.99 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.63 (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 118 PHE 0.023 0.001 PHE A 351 TYR 0.014 0.001 TYR A 136 ARG 0.001 0.000 ARG A 42 *********************** 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 71 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9254 (mt) REVERT: A 89 TYR cc_start: 0.6740 (t80) cc_final: 0.6414 (t80) REVERT: A 124 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8073 (tt) REVERT: A 328 LYS cc_start: 0.6258 (OUTLIER) cc_final: 0.4931 (ptmt) REVERT: A 361 SER cc_start: 0.7460 (p) cc_final: 0.7189 (t) REVERT: A 385 PHE cc_start: 0.8410 (t80) cc_final: 0.8171 (t80) REVERT: A 434 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6772 (mp) outliers start: 15 outliers final: 11 residues processed: 67 average time/residue: 0.1239 time to fit residues: 10.6143 Evaluate side-chains 70 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 177 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 291 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 431 GLN 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: 2.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.0570 overall best weight: 0.5900 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.145560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123850 restraints weight = 5059.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.127106 restraints weight = 3061.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.129418 restraints weight = 2216.301| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3286 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= 0.190 Angle : 0.579 11.359 4384 Z= 0.281 Chirality : 0.039 0.173 509 Planarity : 0.004 0.040 521 Dihedral : 6.828 89.893 440 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.82 % Allowed : 32.83 % 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: 2.15 (0.43), residues: 380 helix: 1.99 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.64 (0.72), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 107 HIS 0.001 0.000 HIS A 27 PHE 0.016 0.001 PHE A 103 TYR 0.014 0.001 TYR A 136 ARG 0.001 0.000 ARG A 42 ********************** 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 70 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9257 (mt) REVERT: A 89 TYR cc_start: 0.6709 (t80) cc_final: 0.6446 (t80) REVERT: A 124 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8092 (tt) REVERT: A 361 SER cc_start: 0.7465 (p) cc_final: 0.7142 (t) REVERT: A 385 PHE cc_start: 0.8425 (t80) cc_final: 0.8167 (t80) REVERT: A 434 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6808 (mp) outliers start: 16 outliers final: 11 residues processed: 66 average time/residue: 0.1316 time to fit residues: 11.2867 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 : 0.403 ------------------------------------------------------------------------------- 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 177 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 431 GLN 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: 0.5980 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.151771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.129950 restraints weight = 4978.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.133757 restraints weight = 2858.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.136216 restraints weight = 1992.551| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3370 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= 0.210 Angle : 0.591 11.190 4384 Z= 0.287 Chirality : 0.039 0.165 509 Planarity : 0.004 0.040 521 Dihedral : 6.807 89.522 440 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.82 % Allowed : 33.13 % 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: 2.12 (0.43), residues: 380 helix: 1.96 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.64 (0.72), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 107 HIS 0.001 0.001 HIS A 27 PHE 0.023 0.001 PHE A 351 TYR 0.034 0.002 TYR A 149 ARG 0.002 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1323.73 seconds wall clock time: 23 minutes 44.71 seconds (1424.71 seconds total)