Starting phenix.real_space_refine on Fri Aug 22 12:38:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5x_38074/08_2025/8x5x_38074.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5x_38074/08_2025/8x5x_38074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x5x_38074/08_2025/8x5x_38074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5x_38074/08_2025/8x5x_38074.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x5x_38074/08_2025/8x5x_38074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5x_38074/08_2025/8x5x_38074.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 1410 2.51 5 N 339 2.21 5 O 337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2105 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2105 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 4 Time building chain proxies: 0.96, per 1000 atoms: 0.46 Number of scatterers: 2105 At special positions: 0 Unit cell: (49.22, 70.62, 72.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 337 8.00 N 339 7.00 C 1410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 180 " distance=2.04 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 444 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 75.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 496 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'B' and resid 29 through 55 removed outlier: 3.861A pdb=" N VAL B 33 " --> pdb=" O PRO B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 Proline residue: B 82 - end of helix removed outlier: 4.414A pdb=" N MET B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 131 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 140 through 157 removed outlier: 3.887A pdb=" N SER B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B 146 " --> pdb=" O THR B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 164 removed outlier: 3.932A pdb=" N ILE B 162 " --> pdb=" O TRP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 221 removed outlier: 5.167A pdb=" N LEU B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 409 through 439 Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 446 through 472 Proline residue: B 465 - end of helix Proline residue: B 469 - end of helix removed outlier: 3.797A pdb=" N ASN B 472 " --> pdb=" O TYR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 481 removed outlier: 3.700A pdb=" N ARG B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) 157 hydrogen bonds defined for protein. 471 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: 0.29 Time building geometry restraints manager: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 608 1.35 - 1.47: 608 1.47 - 1.60: 917 1.60 - 1.72: 0 1.72 - 1.84: 29 Bond restraints: 2162 Sorted by residual: bond pdb=" C ILE B 429 " pdb=" N PRO B 430 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.68e+00 bond pdb=" CG1 ILE B 438 " pdb=" CD1 ILE B 438 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.13e+00 bond pdb=" CG1 ILE B 115 " pdb=" CD1 ILE B 115 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.91e+00 bond pdb=" CB CYS B 180 " pdb=" SG CYS B 180 " ideal model delta sigma weight residual 1.808 1.843 -0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" N GLU B 181 " pdb=" CA GLU B 181 " ideal model delta sigma weight residual 1.468 1.455 0.013 1.24e-02 6.50e+03 1.12e+00 ... (remaining 2157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 2797 1.60 - 3.19: 101 3.19 - 4.79: 23 4.79 - 6.38: 10 6.38 - 7.98: 2 Bond angle restraints: 2933 Sorted by residual: angle pdb=" CA TRP B 455 " pdb=" CB TRP B 455 " pdb=" CG TRP B 455 " ideal model delta sigma weight residual 113.60 118.52 -4.92 1.90e+00 2.77e-01 6.69e+00 angle pdb=" CA LEU B 39 " pdb=" CB LEU B 39 " pdb=" CG LEU B 39 " ideal model delta sigma weight residual 116.30 124.28 -7.98 3.50e+00 8.16e-02 5.20e+00 angle pdb=" C THR B 478 " pdb=" N PHE B 479 " pdb=" CA PHE B 479 " ideal model delta sigma weight residual 121.58 117.23 4.35 1.95e+00 2.63e-01 4.97e+00 angle pdb=" C LEU B 426 " pdb=" N CYS B 427 " pdb=" CA CYS B 427 " ideal model delta sigma weight residual 122.65 119.13 3.52 1.60e+00 3.91e-01 4.85e+00 angle pdb=" N GLY B 96 " pdb=" CA GLY B 96 " pdb=" C GLY B 96 " ideal model delta sigma weight residual 113.18 108.34 4.84 2.37e+00 1.78e-01 4.16e+00 ... (remaining 2928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 1104 16.23 - 32.46: 119 32.46 - 48.69: 34 48.69 - 64.91: 3 64.91 - 81.14: 3 Dihedral angle restraints: 1263 sinusoidal: 504 harmonic: 759 Sorted by residual: dihedral pdb=" CB CYS B 441 " pdb=" SG CYS B 441 " pdb=" SG CYS B 444 " pdb=" CB CYS B 444 " ideal model delta sinusoidal sigma weight residual 93.00 174.14 -81.14 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" SG CYS B 441 " pdb=" CB CYS B 444 " pdb=" SG CYS B 444 " pdb=" CA CYS B 444 " ideal model delta sinusoidal sigma weight residual 79.00 8.82 70.18 1 2.00e+01 2.50e-03 1.59e+01 dihedral pdb=" CA CYS B 427 " pdb=" C CYS B 427 " pdb=" N TRP B 428 " pdb=" CA TRP B 428 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 1260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 208 0.032 - 0.065: 84 0.065 - 0.097: 36 0.097 - 0.129: 10 0.129 - 0.162: 2 Chirality restraints: 340 Sorted by residual: chirality pdb=" CG LEU B 74 " pdb=" CB LEU B 74 " pdb=" CD1 LEU B 74 " pdb=" CD2 LEU B 74 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CB VAL B 79 " pdb=" CA VAL B 79 " pdb=" CG1 VAL B 79 " pdb=" CG2 VAL B 79 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE B 115 " pdb=" N ILE B 115 " pdb=" C ILE B 115 " pdb=" CB ILE B 115 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 337 not shown) Planarity restraints: 344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 455 " -0.020 2.00e-02 2.50e+03 1.56e-02 6.06e+00 pdb=" CG TRP B 455 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 455 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 455 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 455 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 455 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 455 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 455 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 455 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 455 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 428 " 0.016 2.00e-02 2.50e+03 1.25e-02 3.88e+00 pdb=" CG TRP B 428 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 428 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 428 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 428 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 428 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 428 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 428 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 428 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 428 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 479 " 0.013 2.00e-02 2.50e+03 1.33e-02 3.09e+00 pdb=" CG PHE B 479 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 479 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 479 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 479 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 479 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 479 " 0.000 2.00e-02 2.50e+03 ... (remaining 341 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 18 2.66 - 3.22: 2097 3.22 - 3.78: 3431 3.78 - 4.34: 4203 4.34 - 4.90: 6642 Nonbonded interactions: 16391 Sorted by model distance: nonbonded pdb=" OD1 ASN B 63 " pdb=" OH TYR B 468 " model vdw 2.094 3.040 nonbonded pdb=" OH TYR B 65 " pdb=" OG1 THR B 147 " model vdw 2.143 3.040 nonbonded pdb=" OG1 THR B 41 " pdb=" OG1 THR B 462 " model vdw 2.277 3.040 nonbonded pdb=" O TYR B 458 " pdb=" OG SER B 461 " model vdw 2.364 3.040 nonbonded pdb=" ND2 ASN B 45 " pdb=" OD2 ASP B 73 " model vdw 2.406 3.120 ... (remaining 16386 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=0.00 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: 1.500 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.540 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5295 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 : 0.004 0.057 2164 Z= 0.165 Angle : 0.779 7.979 2937 Z= 0.394 Chirality : 0.044 0.162 340 Planarity : 0.005 0.037 344 Dihedral : 14.147 79.862 761 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.43 % Allowed : 0.43 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.56), residues: 246 helix: 1.40 (0.37), residues: 200 sheet: None (None), residues: 0 loop : -2.56 (0.94), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 97 TYR 0.014 0.002 TYR B 185 PHE 0.031 0.002 PHE B 479 TRP 0.042 0.003 TRP B 455 HIS 0.003 0.001 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 2162) covalent geometry : angle 0.77451 ( 2933) SS BOND : bond 0.00523 ( 2) SS BOND : angle 2.32916 ( 4) hydrogen bonds : bond 0.07067 ( 157) hydrogen bonds : angle 4.57808 ( 471) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.096 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.0534 time to fit residues: 3.4943 Evaluate side-chains 41 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.0060 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.191440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.178837 restraints weight = 4898.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.181864 restraints weight = 2811.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.183908 restraints weight = 1828.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.185149 restraints weight = 1307.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.186172 restraints weight = 1032.993| |-----------------------------------------------------------------------------| r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5365 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2164 Z= 0.142 Angle : 0.732 7.747 2937 Z= 0.355 Chirality : 0.042 0.131 340 Planarity : 0.004 0.042 344 Dihedral : 4.993 18.903 275 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.16 % Allowed : 9.91 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.55), residues: 246 helix: 1.37 (0.36), residues: 201 sheet: None (None), residues: 0 loop : -2.53 (0.97), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 53 TYR 0.012 0.002 TYR B 126 PHE 0.025 0.002 PHE B 479 TRP 0.031 0.002 TRP B 455 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2162) covalent geometry : angle 0.72670 ( 2933) SS BOND : bond 0.00448 ( 2) SS BOND : angle 2.46725 ( 4) hydrogen bonds : bond 0.03652 ( 157) hydrogen bonds : angle 4.21255 ( 471) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: B 185 TYR cc_start: 0.2493 (m-10) cc_final: 0.2128 (m-80) REVERT: B 454 ILE cc_start: 0.8375 (mm) cc_final: 0.8149 (mm) REVERT: B 461 SER cc_start: 0.7844 (p) cc_final: 0.7579 (t) outliers start: 5 outliers final: 5 residues processed: 47 average time/residue: 0.0354 time to fit residues: 2.2074 Evaluate side-chains 44 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 204 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 13 optimal weight: 0.0770 chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 0.0000 chunk 8 optimal weight: 0.7980 overall best weight: 0.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 HIS B 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.193143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.180289 restraints weight = 4938.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.183378 restraints weight = 2843.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.185525 restraints weight = 1844.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.186937 restraints weight = 1314.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.187951 restraints weight = 1016.703| |-----------------------------------------------------------------------------| r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5380 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2164 Z= 0.133 Angle : 0.684 7.383 2937 Z= 0.330 Chirality : 0.041 0.128 340 Planarity : 0.004 0.047 344 Dihedral : 4.648 16.767 275 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.02 % Allowed : 16.81 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.55), residues: 246 helix: 1.51 (0.37), residues: 200 sheet: None (None), residues: 0 loop : -2.27 (0.92), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 97 TYR 0.014 0.002 TYR B 468 PHE 0.023 0.001 PHE B 479 TRP 0.024 0.001 TRP B 455 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 2162) covalent geometry : angle 0.68017 ( 2933) SS BOND : bond 0.00338 ( 2) SS BOND : angle 2.16770 ( 4) hydrogen bonds : bond 0.03534 ( 157) hydrogen bonds : angle 4.08592 ( 471) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: B 185 TYR cc_start: 0.2637 (m-10) cc_final: 0.2294 (m-80) REVERT: B 451 MET cc_start: 0.5303 (mmt) cc_final: 0.5081 (mmt) outliers start: 7 outliers final: 5 residues processed: 48 average time/residue: 0.0400 time to fit residues: 2.5008 Evaluate side-chains 39 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 197 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 0.0070 chunk 12 optimal weight: 0.0170 chunk 11 optimal weight: 5.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.193386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.180418 restraints weight = 5034.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.183361 restraints weight = 3046.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.185228 restraints weight = 2078.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.186771 restraints weight = 1577.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.187549 restraints weight = 1230.696| |-----------------------------------------------------------------------------| r_work (final): 0.4604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5420 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2164 Z= 0.132 Angle : 0.703 7.167 2937 Z= 0.337 Chirality : 0.040 0.115 340 Planarity : 0.004 0.045 344 Dihedral : 4.608 16.225 275 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.74 % Allowed : 18.53 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.55), residues: 246 helix: 1.41 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.13 (0.91), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 97 TYR 0.009 0.001 TYR B 468 PHE 0.029 0.002 PHE B 479 TRP 0.021 0.001 TRP B 455 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 2162) covalent geometry : angle 0.69915 ( 2933) SS BOND : bond 0.00351 ( 2) SS BOND : angle 2.15156 ( 4) hydrogen bonds : bond 0.03527 ( 157) hydrogen bonds : angle 4.12277 ( 471) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: B 193 MET cc_start: 0.6507 (ttm) cc_final: 0.6273 (ttm) REVERT: B 451 MET cc_start: 0.5619 (mmt) cc_final: 0.5414 (mmt) outliers start: 11 outliers final: 6 residues processed: 44 average time/residue: 0.0378 time to fit residues: 2.1739 Evaluate side-chains 38 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 204 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.0970 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.191694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.178014 restraints weight = 4934.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.181148 restraints weight = 2896.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.183162 restraints weight = 1958.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.184900 restraints weight = 1476.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.185722 restraints weight = 1140.762| |-----------------------------------------------------------------------------| r_work (final): 0.4583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5473 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2164 Z= 0.134 Angle : 0.695 7.441 2937 Z= 0.337 Chirality : 0.041 0.157 340 Planarity : 0.004 0.045 344 Dihedral : 4.513 15.686 275 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.45 % Allowed : 19.83 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.55), residues: 246 helix: 1.47 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.18 (0.90), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 97 TYR 0.011 0.001 TYR B 468 PHE 0.025 0.002 PHE B 479 TRP 0.020 0.001 TRP B 455 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 2162) covalent geometry : angle 0.69114 ( 2933) SS BOND : bond 0.00366 ( 2) SS BOND : angle 2.01193 ( 4) hydrogen bonds : bond 0.03597 ( 157) hydrogen bonds : angle 4.14495 ( 471) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: B 451 MET cc_start: 0.5587 (mmt) cc_final: 0.5374 (mmt) outliers start: 8 outliers final: 7 residues processed: 46 average time/residue: 0.0422 time to fit residues: 2.4631 Evaluate side-chains 43 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 438 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.0270 chunk 21 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.193453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.179653 restraints weight = 4881.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.182694 restraints weight = 2927.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.185011 restraints weight = 2007.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.186376 restraints weight = 1486.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.187565 restraints weight = 1191.926| |-----------------------------------------------------------------------------| r_work (final): 0.4602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5463 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2164 Z= 0.129 Angle : 0.695 7.505 2937 Z= 0.334 Chirality : 0.041 0.156 340 Planarity : 0.004 0.046 344 Dihedral : 4.467 15.995 275 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.74 % Allowed : 21.55 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.54), residues: 246 helix: 1.54 (0.37), residues: 197 sheet: None (None), residues: 0 loop : -2.74 (0.82), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 97 TYR 0.020 0.002 TYR B 458 PHE 0.025 0.002 PHE B 479 TRP 0.016 0.001 TRP B 455 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 2162) covalent geometry : angle 0.69099 ( 2933) SS BOND : bond 0.00309 ( 2) SS BOND : angle 2.01181 ( 4) hydrogen bonds : bond 0.03580 ( 157) hydrogen bonds : angle 4.17458 ( 471) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.079 Fit side-chains REVERT: B 197 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7901 (tp) REVERT: B 450 HIS cc_start: 0.6493 (OUTLIER) cc_final: 0.5995 (t-90) outliers start: 11 outliers final: 4 residues processed: 44 average time/residue: 0.0377 time to fit residues: 2.1740 Evaluate side-chains 42 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.191754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.178314 restraints weight = 4961.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.181461 restraints weight = 3011.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.183694 restraints weight = 2038.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.185112 restraints weight = 1485.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.186311 restraints weight = 1176.118| |-----------------------------------------------------------------------------| r_work (final): 0.4585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5491 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2164 Z= 0.130 Angle : 0.683 7.256 2937 Z= 0.329 Chirality : 0.040 0.135 340 Planarity : 0.004 0.046 344 Dihedral : 4.648 15.846 275 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.02 % Allowed : 23.71 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.55), residues: 246 helix: 1.64 (0.37), residues: 197 sheet: None (None), residues: 0 loop : -2.81 (0.85), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 97 TYR 0.015 0.001 TYR B 458 PHE 0.023 0.001 PHE B 479 TRP 0.017 0.001 TRP B 455 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 2162) covalent geometry : angle 0.67841 ( 2933) SS BOND : bond 0.00364 ( 2) SS BOND : angle 2.15160 ( 4) hydrogen bonds : bond 0.03552 ( 157) hydrogen bonds : angle 4.23999 ( 471) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.088 Fit side-chains REVERT: B 450 HIS cc_start: 0.6456 (OUTLIER) cc_final: 0.5965 (t-90) outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.0364 time to fit residues: 1.9635 Evaluate side-chains 38 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.187513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.174215 restraints weight = 4994.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.176994 restraints weight = 2969.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.178795 restraints weight = 2021.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.180284 restraints weight = 1536.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.181392 restraints weight = 1209.357| |-----------------------------------------------------------------------------| r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5592 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2164 Z= 0.141 Angle : 0.713 7.510 2937 Z= 0.342 Chirality : 0.041 0.144 340 Planarity : 0.004 0.045 344 Dihedral : 4.716 16.160 275 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.45 % Allowed : 24.14 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.56), residues: 246 helix: 1.53 (0.37), residues: 196 sheet: None (None), residues: 0 loop : -2.54 (0.90), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 97 TYR 0.012 0.002 TYR B 458 PHE 0.023 0.002 PHE B 479 TRP 0.018 0.002 TRP B 455 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 2162) covalent geometry : angle 0.70990 ( 2933) SS BOND : bond 0.00329 ( 2) SS BOND : angle 2.02840 ( 4) hydrogen bonds : bond 0.03889 ( 157) hydrogen bonds : angle 4.33458 ( 471) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.080 Fit side-chains REVERT: B 93 TRP cc_start: 0.4985 (OUTLIER) cc_final: 0.4477 (m-10) REVERT: B 450 HIS cc_start: 0.6616 (OUTLIER) cc_final: 0.6114 (t-90) outliers start: 8 outliers final: 5 residues processed: 41 average time/residue: 0.0407 time to fit residues: 2.1376 Evaluate side-chains 39 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.0060 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.186738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.173961 restraints weight = 5137.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.176590 restraints weight = 3114.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.178628 restraints weight = 2149.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.179634 restraints weight = 1593.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.180802 restraints weight = 1313.321| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5595 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2164 Z= 0.140 Angle : 0.733 9.911 2937 Z= 0.349 Chirality : 0.041 0.136 340 Planarity : 0.004 0.046 344 Dihedral : 4.706 16.380 275 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.45 % Allowed : 25.00 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.55), residues: 246 helix: 1.45 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.24 (0.96), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 53 TYR 0.014 0.001 TYR B 458 PHE 0.025 0.002 PHE B 475 TRP 0.017 0.002 TRP B 455 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 2162) covalent geometry : angle 0.73020 ( 2933) SS BOND : bond 0.00342 ( 2) SS BOND : angle 1.99163 ( 4) hydrogen bonds : bond 0.03809 ( 157) hydrogen bonds : angle 4.40059 ( 471) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.079 Fit side-chains REVERT: B 450 HIS cc_start: 0.6562 (OUTLIER) cc_final: 0.5947 (t-90) outliers start: 8 outliers final: 7 residues processed: 38 average time/residue: 0.0446 time to fit residues: 2.1573 Evaluate side-chains 39 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 165 TRP Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 22 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: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.187304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.174201 restraints weight = 5080.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.177115 restraints weight = 2971.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.179037 restraints weight = 1986.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.180537 restraints weight = 1469.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.181571 restraints weight = 1140.029| |-----------------------------------------------------------------------------| r_work (final): 0.4537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2164 Z= 0.137 Angle : 0.749 9.787 2937 Z= 0.351 Chirality : 0.042 0.134 340 Planarity : 0.004 0.047 344 Dihedral : 4.734 16.506 275 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.45 % Allowed : 25.43 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.55), residues: 246 helix: 1.54 (0.37), residues: 197 sheet: None (None), residues: 0 loop : -2.80 (0.89), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 97 TYR 0.014 0.001 TYR B 458 PHE 0.024 0.002 PHE B 479 TRP 0.014 0.001 TRP B 455 HIS 0.002 0.000 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 2162) covalent geometry : angle 0.74662 ( 2933) SS BOND : bond 0.00294 ( 2) SS BOND : angle 1.91235 ( 4) hydrogen bonds : bond 0.03782 ( 157) hydrogen bonds : angle 4.38126 ( 471) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.081 Fit side-chains REVERT: B 93 TRP cc_start: 0.5174 (OUTLIER) cc_final: 0.4544 (m-10) REVERT: B 450 HIS cc_start: 0.6472 (OUTLIER) cc_final: 0.6083 (t-90) outliers start: 8 outliers final: 6 residues processed: 38 average time/residue: 0.0366 time to fit residues: 1.8459 Evaluate side-chains 39 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 165 TRP Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.0040 overall best weight: 0.4970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.191302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.180505 restraints weight = 5335.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.182576 restraints weight = 3443.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.184134 restraints weight = 2477.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.185226 restraints weight = 1907.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.185956 restraints weight = 1544.437| |-----------------------------------------------------------------------------| r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5560 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2164 Z= 0.133 Angle : 0.730 9.877 2937 Z= 0.342 Chirality : 0.041 0.135 340 Planarity : 0.004 0.047 344 Dihedral : 4.674 16.800 275 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.88 % Allowed : 24.57 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.55), residues: 246 helix: 1.60 (0.37), residues: 197 sheet: None (None), residues: 0 loop : -2.89 (0.88), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 97 TYR 0.013 0.001 TYR B 458 PHE 0.024 0.002 PHE B 479 TRP 0.016 0.001 TRP B 455 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 2162) covalent geometry : angle 0.72727 ( 2933) SS BOND : bond 0.00256 ( 2) SS BOND : angle 1.86400 ( 4) hydrogen bonds : bond 0.03668 ( 157) hydrogen bonds : angle 4.32708 ( 471) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 679.84 seconds wall clock time: 12 minutes 44.58 seconds (764.58 seconds total)