Starting phenix.real_space_refine on Tue Mar 3 10:50:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggx_40024/03_2026/8ggx_40024.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggx_40024/03_2026/8ggx_40024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggx_40024/03_2026/8ggx_40024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggx_40024/03_2026/8ggx_40024.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggx_40024/03_2026/8ggx_40024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggx_40024/03_2026/8ggx_40024.cif" } resolution = 3.6 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= 0.019 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 13 5.16 5 C 1402 2.51 5 N 332 2.21 5 O 360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2107 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2092 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 6, 'ASP:plan': 4, 'GLU:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 79 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: 0.70, per 1000 atoms: 0.33 Number of scatterers: 2107 At special positions: 0 Unit cell: (55.5328, 84.1669, 63.3421, 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 13 16.00 O 360 8.00 N 332 7.00 C 1402 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: 0.20 Conformation dependent library (CDL) restraints added in 86.9 milliseconds 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: 538 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 87.5% 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 'R' and resid 32 through 61 removed outlier: 3.756A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 68 through 96 removed outlier: 4.181A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix removed outlier: 4.182A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N HIS R 93 " --> pdb=" O PHE R 89 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE R 94 " --> pdb=" O GLY R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 4.008A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.814A pdb=" N ALA R 150 " --> pdb=" O THR R 146 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 171 removed outlier: 3.617A pdb=" N ILE R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 187 Processing helix chain 'R' and resid 198 through 208 Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.778A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 299 removed outlier: 4.490A pdb=" N LEU R 275 " --> pdb=" O ALA R 271 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.052A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.610A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 322 removed outlier: 3.696A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 317 through 322' Processing helix chain 'R' and resid 322 through 327 removed outlier: 3.515A pdb=" N CYS R 327 " --> pdb=" O PRO R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 329 through 340 150 hydrogen bonds defined for protein. 447 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: 0.26 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: 638 1.34 - 1.46: 542 1.46 - 1.58: 965 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 2163 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.451 -0.054 2.00e-02 2.50e+03 7.25e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.573 -0.050 2.00e-02 2.50e+03 6.13e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.441 -0.047 2.00e-02 2.50e+03 5.63e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.565 -0.045 2.00e-02 2.50e+03 5.13e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.487 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 2158 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 2833 1.11 - 2.23: 107 2.23 - 3.34: 16 3.34 - 4.46: 9 4.46 - 5.57: 4 Bond angle restraints: 2969 Sorted by residual: angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 120.31 116.98 3.33 1.52e+00 4.33e-01 4.80e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.20 -5.57 3.00e+00 1.11e-01 3.45e+00 angle pdb=" CA VAL R 295 " pdb=" C VAL R 295 " pdb=" N HIS R 296 " ideal model delta sigma weight residual 117.28 119.25 -1.97 1.16e+00 7.43e-01 2.89e+00 angle pdb=" N HIS R 296 " pdb=" CA HIS R 296 " pdb=" CB HIS R 296 " ideal model delta sigma weight residual 110.28 112.78 -2.50 1.55e+00 4.16e-01 2.60e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 115.65 -4.76 3.00e+00 1.11e-01 2.51e+00 ... (remaining 2964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 1113 17.53 - 35.05: 92 35.05 - 52.58: 19 52.58 - 70.11: 2 70.11 - 87.63: 2 Dihedral angle restraints: 1228 sinusoidal: 400 harmonic: 828 Sorted by residual: dihedral pdb=" CA GLN R 299 " pdb=" C GLN R 299 " pdb=" N ASP R 300 " pdb=" CA ASP R 300 " ideal model delta harmonic sigma weight residual -180.00 -162.88 -17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA GLN R 197 " pdb=" C GLN R 197 " pdb=" N ALA R 198 " pdb=" CA ALA R 198 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CB GLU R 180 " pdb=" CG GLU R 180 " pdb=" CD GLU R 180 " pdb=" OE1 GLU R 180 " ideal model delta sinusoidal sigma weight residual 0.00 -87.63 87.63 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 1225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 230 0.034 - 0.067: 101 0.067 - 0.101: 25 0.101 - 0.135: 3 0.135 - 0.168: 1 Chirality restraints: 360 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 2.57 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CA TYR R 326 " pdb=" N TYR R 326 " pdb=" C TYR R 326 " pdb=" CB TYR R 326 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.99e-01 chirality pdb=" CA LEU R 287 " pdb=" N LEU R 287 " pdb=" C LEU R 287 " pdb=" CB LEU R 287 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.11 2.00e-01 2.50e+01 2.76e-01 ... (remaining 357 not shown) Planarity restraints: 362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 173 " -0.010 2.00e-02 2.50e+03 1.01e-02 2.56e+00 pdb=" CG TRP R 173 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP R 173 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 173 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 173 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 173 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP R 173 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO R 168 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 137 " -0.018 5.00e-02 4.00e+02 2.70e-02 1.16e+00 pdb=" N PRO R 138 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO R 138 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 138 " -0.015 5.00e-02 4.00e+02 ... (remaining 359 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1031 2.97 - 3.45: 2339 3.45 - 3.94: 3154 3.94 - 4.42: 3299 4.42 - 4.90: 5590 Nonbonded interactions: 15413 Sorted by model distance: nonbonded pdb=" OE1 GLU R 180 " pdb=" N ALA R 181 " model vdw 2.489 3.120 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.507 3.040 nonbonded pdb=" OE2 GLU R 107 " pdb=" OH TYR R 174 " model vdw 2.558 3.040 nonbonded pdb=" O TRP R 158 " pdb=" OG SER R 161 " model vdw 2.629 3.040 nonbonded pdb=" N THR R 146 " pdb=" O THR R 146 " model vdw 2.646 2.496 ... (remaining 15408 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 4.260 Find NCS groups from input model: 0.020 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 0.054 2163 Z= 0.184 Angle : 0.544 5.572 2969 Z= 0.293 Chirality : 0.039 0.168 360 Planarity : 0.004 0.030 362 Dihedral : 14.257 87.632 690 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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 are not related in a simple way. whole: 2.20 (0.51), residues: 277 helix: 2.53 (0.36), residues: 200 sheet: None (None), residues: 0 loop : -1.62 (0.66), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 221 TYR 0.006 0.001 TYR R 326 PHE 0.014 0.001 PHE R 336 TRP 0.027 0.002 TRP R 173 HIS 0.003 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 2163) covalent geometry : angle 0.54448 ( 2969) hydrogen bonds : bond 0.13608 ( 150) hydrogen bonds : angle 3.95298 ( 447) *********************** 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 50 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.048 Fit side-chains REVERT: R 192 ASP cc_start: 0.7667 (p0) cc_final: 0.7135 (p0) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0402 time to fit residues: 2.4558 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.077 ------------------------------------------------------------------------------- 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: 0.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 178 HIS ** 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 = 0.3870 r_free = 0.3870 target = 0.161252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.144140 restraints weight = 3536.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146746 restraints weight = 2000.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.148665 restraints weight = 1328.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150021 restraints weight = 990.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150894 restraints weight = 798.972| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2163 Z= 0.155 Angle : 0.532 5.342 2969 Z= 0.299 Chirality : 0.039 0.128 360 Planarity : 0.004 0.032 362 Dihedral : 4.784 17.172 309 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.48 % Allowed : 9.45 % Favored : 86.07 % 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 are not related in a simple way. whole: 1.99 (0.52), residues: 277 helix: 2.37 (0.36), residues: 203 sheet: None (None), residues: 0 loop : -1.82 (0.70), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 131 TYR 0.018 0.002 TYR R 185 PHE 0.011 0.001 PHE R 104 TRP 0.017 0.001 TRP R 173 HIS 0.004 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 2163) covalent geometry : angle 0.53220 ( 2969) hydrogen bonds : bond 0.05987 ( 150) hydrogen bonds : angle 3.66020 ( 447) *********************** 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 50 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.075 Fit side-chains REVERT: R 185 TYR cc_start: 0.7967 (m-80) cc_final: 0.7681 (m-80) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 0.0384 time to fit residues: 2.2758 Evaluate side-chains 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 327 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 178 HIS ** 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 = 0.3854 r_free = 0.3854 target = 0.159703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.142454 restraints weight = 3514.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.145003 restraints weight = 2036.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146859 restraints weight = 1377.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148159 restraints weight = 1034.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149129 restraints weight = 835.876| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2163 Z= 0.148 Angle : 0.524 5.324 2969 Z= 0.293 Chirality : 0.039 0.129 360 Planarity : 0.004 0.028 362 Dihedral : 4.783 16.672 309 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 6.47 % Allowed : 12.44 % Favored : 81.09 % 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 are not related in a simple way. whole: 1.90 (0.52), residues: 277 helix: 2.29 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.89 (0.68), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG R 221 TYR 0.018 0.002 TYR R 185 PHE 0.012 0.001 PHE R 104 TRP 0.018 0.001 TRP R 173 HIS 0.002 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 2163) covalent geometry : angle 0.52351 ( 2969) hydrogen bonds : bond 0.05803 ( 150) hydrogen bonds : angle 3.62481 ( 447) *********************** 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 52 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.077 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 48 average time/residue: 0.0385 time to fit residues: 2.3036 Evaluate side-chains 46 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 327 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 0.0060 chunk 3 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.159128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141394 restraints weight = 3465.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.144065 restraints weight = 1978.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.145871 restraints weight = 1329.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.147243 restraints weight = 994.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.147815 restraints weight = 812.365| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2163 Z= 0.136 Angle : 0.504 5.313 2969 Z= 0.283 Chirality : 0.038 0.128 360 Planarity : 0.003 0.026 362 Dihedral : 4.625 16.564 309 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.98 % Allowed : 14.43 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.51), residues: 277 helix: 2.29 (0.36), residues: 205 sheet: None (None), residues: 0 loop : -1.96 (0.67), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG R 221 TYR 0.011 0.001 TYR R 326 PHE 0.008 0.001 PHE R 193 TRP 0.013 0.001 TRP R 173 HIS 0.002 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 2163) covalent geometry : angle 0.50431 ( 2969) hydrogen bonds : bond 0.05486 ( 150) hydrogen bonds : angle 3.60429 ( 447) *********************** 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 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.078 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.0427 time to fit residues: 2.3148 Evaluate side-chains 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.0970 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.163323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145983 restraints weight = 3509.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148698 restraints weight = 1982.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.150681 restraints weight = 1315.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.151982 restraints weight = 979.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.152445 restraints weight = 792.328| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2163 Z= 0.121 Angle : 0.479 5.306 2969 Z= 0.268 Chirality : 0.037 0.125 360 Planarity : 0.003 0.026 362 Dihedral : 4.496 16.446 309 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.48 % Allowed : 15.92 % Favored : 80.60 % 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 are not related in a simple way. whole: 1.96 (0.52), residues: 277 helix: 2.38 (0.36), residues: 205 sheet: None (None), residues: 0 loop : -2.09 (0.65), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG R 131 TYR 0.010 0.001 TYR R 326 PHE 0.007 0.001 PHE R 193 TRP 0.011 0.001 TRP R 173 HIS 0.010 0.002 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 2163) covalent geometry : angle 0.47907 ( 2969) hydrogen bonds : bond 0.04976 ( 150) hydrogen bonds : angle 3.55936 ( 447) *********************** 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 47 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.073 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 0.0429 time to fit residues: 2.4505 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 327 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.161364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.144233 restraints weight = 3496.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.146906 restraints weight = 1979.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.148843 restraints weight = 1325.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150094 restraints weight = 994.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.151159 restraints weight = 808.196| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2163 Z= 0.129 Angle : 0.489 5.295 2969 Z= 0.274 Chirality : 0.038 0.123 360 Planarity : 0.003 0.027 362 Dihedral : 4.532 16.300 309 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.98 % Allowed : 17.91 % Favored : 78.11 % 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 are not related in a simple way. whole: 1.93 (0.52), residues: 277 helix: 2.41 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -2.20 (0.65), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG R 131 TYR 0.008 0.001 TYR R 308 PHE 0.009 0.001 PHE R 193 TRP 0.019 0.001 TRP R 173 HIS 0.004 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 2163) covalent geometry : angle 0.48904 ( 2969) hydrogen bonds : bond 0.05190 ( 150) hydrogen bonds : angle 3.60402 ( 447) *********************** 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 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.076 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 41 average time/residue: 0.0441 time to fit residues: 2.2623 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 327 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 0.0770 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 0.0040 overall best weight: 0.3328 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.165379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.148214 restraints weight = 3457.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.151023 restraints weight = 1935.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.153008 restraints weight = 1274.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.154422 restraints weight = 939.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.155255 restraints weight = 749.706| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2163 Z= 0.113 Angle : 0.467 5.306 2969 Z= 0.261 Chirality : 0.037 0.124 360 Planarity : 0.003 0.027 362 Dihedral : 4.345 16.286 309 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.48 % Allowed : 19.40 % Favored : 77.11 % 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 are not related in a simple way. whole: 2.14 (0.52), residues: 277 helix: 2.41 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -2.10 (0.65), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 131 TYR 0.006 0.001 TYR R 308 PHE 0.007 0.001 PHE R 193 TRP 0.016 0.001 TRP R 173 HIS 0.008 0.002 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 2163) covalent geometry : angle 0.46705 ( 2969) hydrogen bonds : bond 0.04515 ( 150) hydrogen bonds : angle 3.48901 ( 447) *********************** 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 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.076 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 40 average time/residue: 0.0434 time to fit residues: 2.1724 Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 327 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.160877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143605 restraints weight = 3463.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.146212 restraints weight = 1995.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148166 restraints weight = 1338.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.149427 restraints weight = 1006.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.150446 restraints weight = 817.855| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2163 Z= 0.138 Angle : 0.499 5.291 2969 Z= 0.279 Chirality : 0.038 0.124 360 Planarity : 0.003 0.027 362 Dihedral : 4.445 16.214 309 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.98 % Allowed : 21.39 % Favored : 74.63 % 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 are not related in a simple way. whole: 1.97 (0.52), residues: 277 helix: 2.31 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -2.14 (0.66), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 131 TYR 0.009 0.001 TYR R 308 PHE 0.007 0.001 PHE R 193 TRP 0.016 0.001 TRP R 173 HIS 0.007 0.002 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 2163) covalent geometry : angle 0.49908 ( 2969) hydrogen bonds : bond 0.05457 ( 150) hydrogen bonds : angle 3.62253 ( 447) *********************** 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 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.077 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 40 average time/residue: 0.0463 time to fit residues: 2.3197 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.161485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.143951 restraints weight = 3499.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.146615 restraints weight = 1988.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.148508 restraints weight = 1333.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.149822 restraints weight = 996.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.150846 restraints weight = 807.019| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2163 Z= 0.144 Angle : 0.507 5.317 2969 Z= 0.284 Chirality : 0.038 0.125 360 Planarity : 0.003 0.029 362 Dihedral : 4.523 16.560 309 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.99 % Allowed : 22.89 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.51), residues: 277 helix: 2.15 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -2.42 (0.63), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG R 221 TYR 0.009 0.001 TYR R 308 PHE 0.007 0.001 PHE R 289 TRP 0.020 0.001 TRP R 173 HIS 0.008 0.002 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 2163) covalent geometry : angle 0.50702 ( 2969) hydrogen bonds : bond 0.05659 ( 150) hydrogen bonds : angle 3.67774 ( 447) *********************** 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 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.057 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 40 average time/residue: 0.0449 time to fit residues: 2.2386 Evaluate side-chains 38 residues out of total 248 (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 R residue 34 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 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 = 0.3870 r_free = 0.3870 target = 0.160973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143465 restraints weight = 3494.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146197 restraints weight = 1971.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148084 restraints weight = 1321.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.149363 restraints weight = 993.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.150338 restraints weight = 803.352| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2163 Z= 0.137 Angle : 0.517 5.652 2969 Z= 0.285 Chirality : 0.038 0.125 360 Planarity : 0.003 0.029 362 Dihedral : 4.486 16.338 309 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.49 % Allowed : 23.88 % Favored : 73.63 % 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 are not related in a simple way. whole: 1.85 (0.52), residues: 277 helix: 2.23 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -2.21 (0.66), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG R 221 TYR 0.011 0.001 TYR R 185 PHE 0.007 0.001 PHE R 289 TRP 0.018 0.001 TRP R 173 HIS 0.007 0.002 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 2163) covalent geometry : angle 0.51666 ( 2969) hydrogen bonds : bond 0.05467 ( 150) hydrogen bonds : angle 3.61807 ( 447) ********************** 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: 5 poor density : 34 time to evaluate : 0.069 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 39 average time/residue: 0.0352 time to fit residues: 1.7378 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.162378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.145011 restraints weight = 3524.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147678 restraints weight = 1983.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.149536 restraints weight = 1331.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.150945 restraints weight = 994.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151558 restraints weight = 807.818| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2163 Z= 0.136 Angle : 0.515 5.308 2969 Z= 0.286 Chirality : 0.038 0.125 360 Planarity : 0.003 0.029 362 Dihedral : 4.480 16.517 309 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.49 % Allowed : 24.88 % Favored : 72.64 % 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 are not related in a simple way. whole: 1.79 (0.52), residues: 277 helix: 2.30 (0.36), residues: 205 sheet: None (None), residues: 0 loop : -2.31 (0.66), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG R 221 TYR 0.011 0.001 TYR R 185 PHE 0.007 0.001 PHE R 289 TRP 0.020 0.001 TRP R 173 HIS 0.007 0.002 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 2163) covalent geometry : angle 0.51490 ( 2969) hydrogen bonds : bond 0.05397 ( 150) hydrogen bonds : angle 3.59175 ( 447) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 648.15 seconds wall clock time: 11 minutes 39.40 seconds (699.40 seconds total)