Starting phenix.real_space_refine on Mon Feb 10 20:24:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggk_40011/02_2025/8ggk_40011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggk_40011/02_2025/8ggk_40011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggk_40011/02_2025/8ggk_40011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggk_40011/02_2025/8ggk_40011.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggk_40011/02_2025/8ggk_40011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggk_40011/02_2025/8ggk_40011.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 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 16 5.16 5 C 1479 2.51 5 N 353 2.21 5 O 370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2218 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2201 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 82 Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 2.67, per 1000 atoms: 1.20 Number of scatterers: 2218 At special positions: 0 Unit cell: (59.0036, 86.77, 62.4744, 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 16 16.00 O 370 8.00 N 353 7.00 C 1479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 270.9 milliseconds 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 552 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 87.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 30 through 61 removed outlier: 3.680A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.553A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.768A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 148 through 166 removed outlier: 3.687A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE R 154 " --> pdb=" O ALA R 150 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 178 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 269 through 281 Processing helix chain 'R' and resid 282 through 287 Processing helix chain 'R' and resid 288 through 299 removed outlier: 3.545A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.691A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 340 166 hydrogen bonds defined for protein. 498 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: 0.54 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 660 1.35 - 1.46: 608 1.46 - 1.58: 984 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 2274 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.39e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.566 -0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.436 -0.042 2.00e-02 2.50e+03 4.46e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.559 -0.039 2.00e-02 2.50e+03 3.87e+00 bond pdb=" CAD G1I R 501 " pdb=" OAK G1I R 501 " ideal model delta sigma weight residual 1.353 1.319 0.034 2.00e-02 2.50e+03 2.90e+00 ... (remaining 2269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 2985 1.11 - 2.22: 100 2.22 - 3.33: 15 3.33 - 4.44: 7 4.44 - 5.55: 7 Bond angle restraints: 3114 Sorted by residual: angle pdb=" C HIS R 241 " pdb=" N VAL R 242 " pdb=" CA VAL R 242 " ideal model delta sigma weight residual 121.70 125.97 -4.27 1.80e+00 3.09e-01 5.64e+00 angle pdb=" N VAL R 87 " pdb=" CA VAL R 87 " pdb=" C VAL R 87 " ideal model delta sigma weight residual 108.88 112.82 -3.94 2.16e+00 2.14e-01 3.33e+00 angle pdb=" N SER R 207 " pdb=" CA SER R 207 " pdb=" C SER R 207 " ideal model delta sigma weight residual 111.69 113.86 -2.17 1.23e+00 6.61e-01 3.11e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 117.69 -5.06 3.00e+00 1.11e-01 2.84e+00 angle pdb=" C THR R 96 " pdb=" N LYS R 97 " pdb=" CA LYS R 97 " ideal model delta sigma weight residual 124.31 127.11 -2.80 1.67e+00 3.59e-01 2.80e+00 ... (remaining 3109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.74: 1081 10.74 - 21.47: 139 21.47 - 32.20: 55 32.20 - 42.93: 23 42.93 - 53.67: 5 Dihedral angle restraints: 1303 sinusoidal: 454 harmonic: 849 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 -159.29 -20.71 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA HIS R 178 " pdb=" C HIS R 178 " pdb=" N GLN R 179 " pdb=" CA GLN R 179 " ideal model delta harmonic sigma weight residual -180.00 -163.07 -16.93 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CG ARG R 328 " pdb=" CD ARG R 328 " pdb=" NE ARG R 328 " pdb=" CZ ARG R 328 " ideal model delta sinusoidal sigma weight residual 180.00 136.83 43.17 2 1.50e+01 4.44e-03 9.99e+00 ... (remaining 1300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 214 0.030 - 0.060: 117 0.060 - 0.090: 36 0.090 - 0.120: 14 0.120 - 0.151: 1 Chirality restraints: 382 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 2.55 -0.15 2.00e-01 2.50e+01 5.67e-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 2.40 0.11 2.00e-01 2.50e+01 2.80e-01 chirality pdb=" CA ASN R 322 " pdb=" N ASN R 322 " pdb=" C ASN R 322 " pdb=" CB ASN R 322 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.60e-01 ... (remaining 379 not shown) Planarity restraints: 372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " 0.014 5.00e-02 4.00e+02 2.05e-02 6.74e-01 pdb=" N PRO R 323 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.013 5.00e-02 4.00e+02 1.97e-02 6.23e-01 pdb=" N PRO R 211 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.013 5.00e-02 4.00e+02 1.93e-02 5.95e-01 pdb=" N PRO R 168 " 0.033 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.011 5.00e-02 4.00e+02 ... (remaining 369 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 512 2.79 - 3.32: 2157 3.32 - 3.84: 3513 3.84 - 4.37: 3734 4.37 - 4.90: 6864 Nonbonded interactions: 16780 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR R 174 " pdb=" O HOH R 601 " model vdw 2.270 3.040 nonbonded pdb=" O SER R 111 " pdb=" OG SER R 165 " model vdw 2.292 3.040 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.401 3.120 nonbonded pdb=" N HIS R 178 " pdb=" O HIS R 178 " model vdw 2.641 2.496 ... (remaining 16775 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.230 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 0.051 2274 Z= 0.277 Angle : 0.550 5.548 3114 Z= 0.299 Chirality : 0.040 0.151 382 Planarity : 0.003 0.021 372 Dihedral : 12.874 53.666 748 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.52), residues: 284 helix: 2.00 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -1.34 (0.75), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.009 0.001 PHE R 104 TYR 0.008 0.001 TYR R 209 ARG 0.002 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.252 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.2323 time to fit residues: 7.1760 Evaluate side-chains 22 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 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 = 0.3205 r_free = 0.3205 target = 0.115461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.101180 restraints weight = 2999.121| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.61 r_work: 0.2928 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2274 Z= 0.231 Angle : 0.511 5.628 3114 Z= 0.284 Chirality : 0.039 0.109 382 Planarity : 0.003 0.023 372 Dihedral : 4.415 21.084 320 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 2.22 % Allowed : 5.33 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.51), residues: 284 helix: 1.98 (0.35), residues: 220 sheet: None (None), residues: 0 loop : -1.38 (0.81), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.009 0.001 PHE R 61 TYR 0.007 0.001 TYR R 308 ARG 0.002 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.198 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.1967 time to fit residues: 5.7396 Evaluate side-chains 24 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.116810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.102239 restraints weight = 2980.574| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.67 r_work: 0.2933 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2274 Z= 0.199 Angle : 0.482 5.533 3114 Z= 0.266 Chirality : 0.038 0.103 382 Planarity : 0.003 0.022 372 Dihedral : 4.362 20.916 320 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 2.67 % Allowed : 8.44 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.51), residues: 284 helix: 2.04 (0.35), residues: 221 sheet: None (None), residues: 0 loop : -1.22 (0.82), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.007 0.001 PHE R 104 TYR 0.007 0.001 TYR R 308 ARG 0.001 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.240 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 25 average time/residue: 0.1981 time to fit residues: 5.8041 Evaluate side-chains 24 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 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 = 0.3207 r_free = 0.3207 target = 0.115785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.101326 restraints weight = 2992.124| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.62 r_work: 0.2928 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2274 Z= 0.216 Angle : 0.484 5.506 3114 Z= 0.267 Chirality : 0.038 0.103 382 Planarity : 0.003 0.023 372 Dihedral : 4.351 20.811 320 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.78 % Allowed : 11.11 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.52), residues: 284 helix: 2.11 (0.35), residues: 220 sheet: None (None), residues: 0 loop : -1.40 (0.80), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.008 0.001 PHE R 61 TYR 0.007 0.001 TYR R 209 ARG 0.001 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.255 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 25 average time/residue: 0.2037 time to fit residues: 5.9990 Evaluate side-chains 25 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU 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 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 27 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.0870 chunk 18 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.119039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.104400 restraints weight = 3018.630| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.68 r_work: 0.2964 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2274 Z= 0.165 Angle : 0.454 5.433 3114 Z= 0.250 Chirality : 0.037 0.102 382 Planarity : 0.003 0.022 372 Dihedral : 4.178 20.701 320 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.78 % Allowed : 11.11 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.52), residues: 284 helix: 2.25 (0.35), residues: 220 sheet: None (None), residues: 0 loop : -1.30 (0.81), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.007 0.001 PHE R 104 TYR 0.006 0.001 TYR R 209 ARG 0.001 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.244 Fit side-chains REVERT: R 227 LYS cc_start: 0.8072 (tttt) cc_final: 0.7719 (ttmm) REVERT: R 231 GLN cc_start: 0.7985 (tt0) cc_final: 0.7763 (tm-30) outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 0.2241 time to fit residues: 6.9759 Evaluate side-chains 27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 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 = 0.3205 r_free = 0.3205 target = 0.115375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.100688 restraints weight = 3010.740| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.65 r_work: 0.2919 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2274 Z= 0.226 Angle : 0.486 5.483 3114 Z= 0.267 Chirality : 0.038 0.103 382 Planarity : 0.003 0.022 372 Dihedral : 4.290 20.667 320 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.67 % Allowed : 11.56 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.52), residues: 284 helix: 2.17 (0.36), residues: 220 sheet: None (None), residues: 0 loop : -1.42 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.009 0.001 PHE R 61 TYR 0.007 0.001 TYR R 209 ARG 0.002 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.224 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 27 average time/residue: 0.2029 time to fit residues: 6.4419 Evaluate side-chains 27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.116848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.102383 restraints weight = 3037.095| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.59 r_work: 0.2947 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2274 Z= 0.194 Angle : 0.473 5.433 3114 Z= 0.259 Chirality : 0.038 0.103 382 Planarity : 0.003 0.022 372 Dihedral : 4.211 20.769 320 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 2.22 % Allowed : 12.89 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.52), residues: 284 helix: 2.21 (0.35), residues: 221 sheet: None (None), residues: 0 loop : -1.30 (0.79), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.007 0.001 PHE R 104 TYR 0.006 0.001 TYR R 209 ARG 0.001 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.254 Fit side-chains REVERT: R 231 GLN cc_start: 0.7881 (tt0) cc_final: 0.7641 (tm-30) outliers start: 5 outliers final: 4 residues processed: 27 average time/residue: 0.1867 time to fit residues: 5.9461 Evaluate side-chains 27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 = 0.3187 r_free = 0.3187 target = 0.114028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.099469 restraints weight = 3089.636| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.62 r_work: 0.2904 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2274 Z= 0.243 Angle : 0.499 5.489 3114 Z= 0.275 Chirality : 0.039 0.105 382 Planarity : 0.003 0.022 372 Dihedral : 4.342 20.710 320 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.22 % Allowed : 12.89 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.51), residues: 284 helix: 2.14 (0.35), residues: 220 sheet: None (None), residues: 0 loop : -1.44 (0.76), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.009 0.001 PHE R 61 TYR 0.007 0.001 TYR R 209 ARG 0.002 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.227 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 25 average time/residue: 0.1306 time to fit residues: 4.0923 Evaluate side-chains 25 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU 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 11 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3209 r_free = 0.3209 target = 0.115708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.101072 restraints weight = 3027.782| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.64 r_work: 0.2922 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2274 Z= 0.206 Angle : 0.481 5.455 3114 Z= 0.265 Chirality : 0.038 0.108 382 Planarity : 0.003 0.022 372 Dihedral : 4.258 20.825 320 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 2.67 % Allowed : 12.89 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.51), residues: 284 helix: 2.16 (0.35), residues: 220 sheet: None (None), residues: 0 loop : -1.42 (0.76), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.008 0.001 PHE R 61 TYR 0.006 0.001 TYR R 308 ARG 0.001 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.234 Fit side-chains REVERT: R 231 GLN cc_start: 0.7927 (tt0) cc_final: 0.7677 (tm-30) outliers start: 6 outliers final: 6 residues processed: 27 average time/residue: 0.1771 time to fit residues: 5.6538 Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU 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 16 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3232 r_free = 0.3232 target = 0.117416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.102752 restraints weight = 2967.030| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.64 r_work: 0.2948 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2274 Z= 0.182 Angle : 0.464 5.435 3114 Z= 0.255 Chirality : 0.038 0.105 382 Planarity : 0.003 0.022 372 Dihedral : 4.176 20.763 320 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.78 % Allowed : 13.78 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.51), residues: 284 helix: 2.21 (0.35), residues: 221 sheet: None (None), residues: 0 loop : -1.34 (0.78), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.007 0.001 PHE R 61 TYR 0.006 0.001 TYR R 308 ARG 0.001 0.000 ARG R 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.251 Fit side-chains REVERT: R 227 LYS cc_start: 0.8046 (tttt) cc_final: 0.7685 (ttmm) REVERT: R 231 GLN cc_start: 0.7988 (tt0) cc_final: 0.7761 (tm-30) outliers start: 4 outliers final: 4 residues processed: 27 average time/residue: 0.2263 time to fit residues: 7.0762 Evaluate side-chains 27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU 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 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3196 r_free = 0.3196 target = 0.114724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.100103 restraints weight = 3002.716| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.66 r_work: 0.2907 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2274 Z= 0.228 Angle : 0.488 5.471 3114 Z= 0.269 Chirality : 0.039 0.108 382 Planarity : 0.003 0.022 372 Dihedral : 4.284 20.673 320 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.67 % Allowed : 12.89 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.51), residues: 284 helix: 2.16 (0.35), residues: 220 sheet: None (None), residues: 0 loop : -1.45 (0.76), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.008 0.001 PHE R 61 TYR 0.007 0.001 TYR R 209 ARG 0.001 0.000 ARG R 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1563.65 seconds wall clock time: 28 minutes 23.77 seconds (1703.77 seconds total)