Starting phenix.real_space_refine on Fri Aug 22 12:39:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggz_40026/08_2025/8ggz_40026.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggz_40026/08_2025/8ggz_40026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ggz_40026/08_2025/8ggz_40026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggz_40026/08_2025/8ggz_40026.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ggz_40026/08_2025/8ggz_40026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggz_40026/08_2025/8ggz_40026.map" } resolution = 3.9 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= 0.017 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 9 5.16 5 C 1324 2.51 5 N 327 2.21 5 O 334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 1994 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1979 Classifications: {'peptide': 281} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 90} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 359 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'TRP:plan': 1, 'ASN:plan1': 4, 'ARG:plan': 6, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 9, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.49, per 1000 atoms: 0.75 Number of scatterers: 1994 At special positions: 0 Unit cell: (56.4005, 85.0346, 61.6067, 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 9 16.00 O 334 8.00 N 327 7.00 C 1324 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: 0.32 Conformation dependent library (CDL) restraints added in 155.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 536 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 85.1% 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 'R' and resid 32 through 61 removed outlier: 3.941A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 86 removed outlier: 4.307A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.938A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.602A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 181 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 270 through 297 removed outlier: 4.013A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.934A pdb=" N VAL R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 316 Processing helix chain 'R' and resid 317 through 320 Processing helix chain 'R' and resid 321 through 326 Processing helix chain 'R' and resid 329 through 338 162 hydrogen bonds defined for protein. 483 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: 0.28 Time building geometry restraints manager: 0.39 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: 615 1.34 - 1.46: 532 1.46 - 1.58: 889 1.58 - 1.69: 0 1.69 - 1.81: 13 Bond restraints: 2049 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.452 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.574 -0.051 2.00e-02 2.50e+03 6.54e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.443 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.564 -0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " ideal model delta sigma weight residual 1.506 1.542 -0.036 2.00e-02 2.50e+03 3.17e+00 ... (remaining 2044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 2674 1.12 - 2.24: 111 2.24 - 3.36: 24 3.36 - 4.48: 5 4.48 - 5.60: 6 Bond angle restraints: 2820 Sorted by residual: angle pdb=" C GLU R 180 " pdb=" N ALA R 181 " pdb=" CA ALA R 181 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.60e+00 angle pdb=" C THR R 96 " pdb=" N LYS R 97 " pdb=" CA LYS R 97 " ideal model delta sigma weight residual 123.05 126.25 -3.20 1.57e+00 4.06e-01 4.16e+00 angle pdb=" C TRP R 173 " pdb=" N TYR R 174 " pdb=" CA TYR R 174 " ideal model delta sigma weight residual 123.91 127.07 -3.16 1.66e+00 3.63e-01 3.63e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.10 -5.47 3.00e+00 1.11e-01 3.32e+00 angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 120.29 117.75 2.54 1.42e+00 4.96e-01 3.19e+00 ... (remaining 2815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 1044 15.45 - 30.90: 80 30.90 - 46.35: 23 46.35 - 61.79: 1 61.79 - 77.24: 2 Dihedral angle restraints: 1150 sinusoidal: 324 harmonic: 826 Sorted by residual: dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual 180.00 -162.20 -17.80 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ARG R 131 " pdb=" CB ARG R 131 " pdb=" CG ARG R 131 " pdb=" CD ARG R 131 " ideal model delta sinusoidal sigma weight residual -180.00 -128.30 -51.70 3 1.50e+01 4.44e-03 9.04e+00 dihedral pdb=" CA MET R 82 " pdb=" CB MET R 82 " pdb=" CG MET R 82 " pdb=" SD MET R 82 " ideal model delta sinusoidal sigma weight residual 180.00 -134.27 -45.73 3 1.50e+01 4.44e-03 8.22e+00 ... (remaining 1147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 235 0.036 - 0.072: 87 0.072 - 0.108: 14 0.108 - 0.143: 1 0.143 - 0.179: 1 Chirality restraints: 338 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.58 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CA TYR R 174 " pdb=" N TYR R 174 " pdb=" C TYR R 174 " pdb=" CB TYR R 174 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.04e-01 chirality pdb=" CA TRP R 286 " pdb=" N TRP R 286 " pdb=" C TRP R 286 " pdb=" CB TRP R 286 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.75e-01 ... (remaining 335 not shown) Planarity restraints: 350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER R 137 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO R 138 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 138 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 138 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 108 " 0.009 2.00e-02 2.50e+03 8.48e-03 1.26e+00 pdb=" CG PHE R 108 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE R 108 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE R 108 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE R 108 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 108 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE R 108 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 173 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.07e+00 pdb=" C TRP R 173 " -0.018 2.00e-02 2.50e+03 pdb=" O TRP R 173 " 0.007 2.00e-02 2.50e+03 pdb=" N TYR R 174 " 0.006 2.00e-02 2.50e+03 ... (remaining 347 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 512 2.80 - 3.33: 2010 3.33 - 3.85: 3195 3.85 - 4.38: 2923 4.38 - 4.90: 5562 Nonbonded interactions: 14202 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.278 3.040 nonbonded pdb=" O LEU R 324 " pdb=" NH1 ARG R 328 " model vdw 2.366 3.120 nonbonded pdb=" OD1 ASP R 192 " pdb=" N PHE R 193 " model vdw 2.386 3.120 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.529 3.120 nonbonded pdb=" N THR R 146 " pdb=" O THR R 146 " model vdw 2.633 2.496 ... (remaining 14197 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 6.410 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 0.055 2049 Z= 0.194 Angle : 0.580 5.601 2820 Z= 0.326 Chirality : 0.038 0.179 338 Planarity : 0.004 0.055 350 Dihedral : 12.741 77.243 614 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.26 (0.53), residues: 277 helix: 2.79 (0.37), residues: 200 sheet: None (None), residues: 0 loop : -2.26 (0.62), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 131 TYR 0.010 0.001 TYR R 219 PHE 0.019 0.001 PHE R 108 TRP 0.011 0.001 TRP R 109 HIS 0.004 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 2049) covalent geometry : angle 0.57963 ( 2820) hydrogen bonds : bond 0.13636 ( 162) hydrogen bonds : angle 4.75481 ( 483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.076 Fit side-chains REVERT: R 131 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7616 (mtp85) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0458 time to fit residues: 2.7605 Evaluate side-chains 33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.0770 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.0670 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.150230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.135611 restraints weight = 3661.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.138567 restraints weight = 1873.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140650 restraints weight = 1147.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141878 restraints weight = 792.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.142971 restraints weight = 607.001| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2049 Z= 0.114 Angle : 0.485 4.736 2820 Z= 0.264 Chirality : 0.038 0.119 338 Planarity : 0.004 0.040 350 Dihedral : 3.769 17.904 309 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 6.37 % Allowed : 14.01 % Favored : 79.62 % 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: 2.51 (0.54), residues: 277 helix: 2.71 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -2.00 (0.74), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 328 TYR 0.017 0.002 TYR R 308 PHE 0.015 0.001 PHE R 289 TRP 0.008 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 2049) covalent geometry : angle 0.48489 ( 2820) hydrogen bonds : bond 0.04391 ( 162) hydrogen bonds : angle 3.74910 ( 483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.080 Fit side-chains REVERT: R 131 ARG cc_start: 0.8010 (mtm-85) cc_final: 0.7416 (ttt90) outliers start: 10 outliers final: 8 residues processed: 40 average time/residue: 0.0473 time to fit residues: 2.3393 Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.0060 chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.147274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132523 restraints weight = 3778.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135396 restraints weight = 1958.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.137447 restraints weight = 1209.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.138814 restraints weight = 842.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139817 restraints weight = 638.840| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2049 Z= 0.124 Angle : 0.489 4.794 2820 Z= 0.269 Chirality : 0.038 0.120 338 Planarity : 0.004 0.043 350 Dihedral : 3.777 17.600 309 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.10 % Allowed : 20.38 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.60 (0.53), residues: 277 helix: 2.82 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -1.90 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 328 TYR 0.014 0.001 TYR R 141 PHE 0.010 0.001 PHE R 108 TRP 0.010 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 2049) covalent geometry : angle 0.48862 ( 2820) hydrogen bonds : bond 0.04642 ( 162) hydrogen bonds : angle 3.66074 ( 483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.079 Fit side-chains REVERT: R 131 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7455 (ttt90) outliers start: 8 outliers final: 8 residues processed: 35 average time/residue: 0.0491 time to fit residues: 2.1198 Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.144995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.130476 restraints weight = 3731.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133192 restraints weight = 1939.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.135161 restraints weight = 1206.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136516 restraints weight = 847.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137478 restraints weight = 645.359| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2049 Z= 0.123 Angle : 0.491 5.559 2820 Z= 0.267 Chirality : 0.038 0.120 338 Planarity : 0.004 0.042 350 Dihedral : 3.778 17.778 309 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 7.01 % Allowed : 19.75 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.57 (0.54), residues: 277 helix: 2.67 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -1.88 (0.80), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 328 TYR 0.012 0.001 TYR R 308 PHE 0.010 0.001 PHE R 289 TRP 0.011 0.001 TRP R 109 HIS 0.005 0.002 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 2049) covalent geometry : angle 0.49053 ( 2820) hydrogen bonds : bond 0.04786 ( 162) hydrogen bonds : angle 3.61212 ( 483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.076 Fit side-chains REVERT: R 131 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7435 (ttt90) outliers start: 11 outliers final: 8 residues processed: 39 average time/residue: 0.0529 time to fit residues: 2.4973 Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.143078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128534 restraints weight = 3726.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131271 restraints weight = 1931.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.133144 restraints weight = 1196.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134506 restraints weight = 842.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.135346 restraints weight = 647.854| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2049 Z= 0.130 Angle : 0.503 4.771 2820 Z= 0.276 Chirality : 0.039 0.122 338 Planarity : 0.003 0.038 350 Dihedral : 3.885 18.026 309 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 7.01 % Allowed : 20.38 % Favored : 72.61 % 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: 2.53 (0.54), residues: 277 helix: 2.64 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -1.90 (0.80), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 328 TYR 0.013 0.002 TYR R 141 PHE 0.010 0.001 PHE R 289 TRP 0.010 0.001 TRP R 109 HIS 0.005 0.002 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 2049) covalent geometry : angle 0.50269 ( 2820) hydrogen bonds : bond 0.04927 ( 162) hydrogen bonds : angle 3.65612 ( 483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.080 Fit side-chains REVERT: R 131 ARG cc_start: 0.8092 (mtm-85) cc_final: 0.7470 (ttt90) outliers start: 11 outliers final: 10 residues processed: 35 average time/residue: 0.0498 time to fit residues: 2.1547 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.0000 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.129141 restraints weight = 3681.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.131854 restraints weight = 1918.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.133785 restraints weight = 1193.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135057 restraints weight = 835.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.136026 restraints weight = 643.200| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2049 Z= 0.120 Angle : 0.484 4.736 2820 Z= 0.265 Chirality : 0.038 0.121 338 Planarity : 0.003 0.033 350 Dihedral : 3.838 17.996 309 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 6.37 % Allowed : 22.29 % Favored : 71.34 % 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: 2.49 (0.54), residues: 277 helix: 2.57 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.82 (0.83), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 328 TYR 0.011 0.001 TYR R 308 PHE 0.010 0.001 PHE R 289 TRP 0.011 0.001 TRP R 109 HIS 0.005 0.002 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 2049) covalent geometry : angle 0.48432 ( 2820) hydrogen bonds : bond 0.04724 ( 162) hydrogen bonds : angle 3.58515 ( 483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.086 Fit side-chains REVERT: R 131 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.7457 (ttt90) outliers start: 10 outliers final: 10 residues processed: 35 average time/residue: 0.0498 time to fit residues: 2.1198 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 0.0060 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.143200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128792 restraints weight = 3700.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131583 restraints weight = 1936.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.133385 restraints weight = 1201.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.134820 restraints weight = 849.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135655 restraints weight = 646.576| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2049 Z= 0.120 Angle : 0.484 4.734 2820 Z= 0.266 Chirality : 0.038 0.121 338 Planarity : 0.003 0.033 350 Dihedral : 3.869 18.038 309 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 7.01 % Allowed : 21.66 % Favored : 71.34 % 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: 2.51 (0.54), residues: 277 helix: 2.54 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -1.70 (0.88), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 328 TYR 0.013 0.001 TYR R 141 PHE 0.009 0.001 PHE R 289 TRP 0.010 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 2049) covalent geometry : angle 0.48385 ( 2820) hydrogen bonds : bond 0.04723 ( 162) hydrogen bonds : angle 3.57953 ( 483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.078 Fit side-chains REVERT: R 131 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7453 (ttt90) outliers start: 11 outliers final: 11 residues processed: 36 average time/residue: 0.0612 time to fit residues: 2.5987 Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 3 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131310 restraints weight = 3753.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.134146 restraints weight = 1964.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136113 restraints weight = 1210.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.137354 restraints weight = 841.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.138316 restraints weight = 647.360| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2049 Z= 0.113 Angle : 0.474 4.697 2820 Z= 0.259 Chirality : 0.038 0.120 338 Planarity : 0.003 0.031 350 Dihedral : 3.797 17.916 309 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 7.01 % Allowed : 21.66 % Favored : 71.34 % 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: 2.55 (0.55), residues: 277 helix: 2.57 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -1.68 (0.89), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 328 TYR 0.011 0.001 TYR R 174 PHE 0.008 0.001 PHE R 289 TRP 0.010 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 2049) covalent geometry : angle 0.47401 ( 2820) hydrogen bonds : bond 0.04457 ( 162) hydrogen bonds : angle 3.56057 ( 483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.077 Fit side-chains REVERT: R 131 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7412 (ttt90) outliers start: 11 outliers final: 11 residues processed: 36 average time/residue: 0.0473 time to fit residues: 2.1071 Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 6 optimal weight: 0.0020 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.0070 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.0170 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.0670 chunk 21 optimal weight: 0.5980 overall best weight: 0.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138856 restraints weight = 3562.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.141701 restraints weight = 1843.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.143695 restraints weight = 1132.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145119 restraints weight = 788.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.146173 restraints weight = 595.610| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2049 Z= 0.099 Angle : 0.454 4.715 2820 Z= 0.242 Chirality : 0.038 0.131 338 Planarity : 0.003 0.031 350 Dihedral : 3.619 17.516 309 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.82 % Allowed : 25.48 % Favored : 70.70 % 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: 2.63 (0.54), residues: 277 helix: 2.70 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.90 (0.85), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG R 328 TYR 0.014 0.001 TYR R 141 PHE 0.007 0.001 PHE R 108 TRP 0.009 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00179 ( 2049) covalent geometry : angle 0.45429 ( 2820) hydrogen bonds : bond 0.03243 ( 162) hydrogen bonds : angle 3.40054 ( 483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.056 Fit side-chains REVERT: R 131 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7335 (ttt90) outliers start: 6 outliers final: 6 residues processed: 35 average time/residue: 0.0496 time to fit residues: 2.1563 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.0980 chunk 7 optimal weight: 0.0270 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 0.0170 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 0 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136824 restraints weight = 3698.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139700 restraints weight = 1927.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141863 restraints weight = 1188.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143184 restraints weight = 817.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144221 restraints weight = 618.708| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2049 Z= 0.098 Angle : 0.452 4.685 2820 Z= 0.242 Chirality : 0.037 0.126 338 Planarity : 0.004 0.052 350 Dihedral : 3.552 16.815 309 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.46 % Allowed : 24.84 % Favored : 70.70 % 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: 2.60 (0.54), residues: 277 helix: 2.70 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.02 (0.82), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 328 TYR 0.012 0.001 TYR R 174 PHE 0.006 0.001 PHE R 108 TRP 0.007 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 2049) covalent geometry : angle 0.45182 ( 2820) hydrogen bonds : bond 0.03455 ( 162) hydrogen bonds : angle 3.39065 ( 483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.074 Fit side-chains REVERT: R 131 ARG cc_start: 0.7957 (mtm-85) cc_final: 0.7372 (ttt90) outliers start: 7 outliers final: 6 residues processed: 36 average time/residue: 0.0470 time to fit residues: 2.0889 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128182 restraints weight = 3781.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130845 restraints weight = 2000.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132845 restraints weight = 1255.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134033 restraints weight = 881.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.134997 restraints weight = 685.836| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2049 Z= 0.138 Angle : 0.513 4.818 2820 Z= 0.283 Chirality : 0.039 0.121 338 Planarity : 0.004 0.055 350 Dihedral : 3.810 16.885 309 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.82 % Allowed : 26.11 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.51 (0.54), residues: 277 helix: 2.64 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.03 (0.79), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 328 TYR 0.014 0.002 TYR R 141 PHE 0.008 0.001 PHE R 290 TRP 0.008 0.001 TRP R 109 HIS 0.010 0.003 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 2049) covalent geometry : angle 0.51276 ( 2820) hydrogen bonds : bond 0.04960 ( 162) hydrogen bonds : angle 3.66862 ( 483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 629.84 seconds wall clock time: 11 minutes 37.48 seconds (697.48 seconds total)