Starting phenix.real_space_refine on Wed Mar 5 14:49:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggw_40023/03_2025/8ggw_40023.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggw_40023/03_2025/8ggw_40023.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/8ggw_40023/03_2025/8ggw_40023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggw_40023/03_2025/8ggw_40023.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggw_40023/03_2025/8ggw_40023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggw_40023/03_2025/8ggw_40023.cif" } resolution = 3.6 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= 0.020 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 12 5.16 5 C 1379 2.51 5 N 335 2.21 5 O 353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2079 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2064 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 80 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: 2.64, per 1000 atoms: 1.27 Number of scatterers: 2079 At special positions: 0 Unit cell: (54.6651, 83.2992, 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 12 16.00 O 353 8.00 N 335 7.00 C 1379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.04 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: 0.55 Conformation dependent library (CDL) restraints added in 269.3 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: 12 helices and 0 sheets defined 85.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.627A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE R 58 " --> pdb=" O VAL R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 3.940A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix removed outlier: 3.643A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS R 93 " --> pdb=" O PHE R 89 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE R 94 " --> pdb=" O GLY R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 137 removed outlier: 3.847A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER R 120 " --> pdb=" O CYS R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.790A pdb=" N ALA R 150 " --> pdb=" O THR R 146 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.619A 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: 3.883A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 299 Proline residue: R 288 - end of helix removed outlier: 3.918A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.874A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 327 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 161 hydrogen bonds defined for protein. 483 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.59 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 - 1.34: 638 1.34 - 1.46: 583 1.46 - 1.58: 897 1.58 - 1.70: 0 1.70 - 1.82: 17 Bond restraints: 2135 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 7.18e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.440 -0.046 2.00e-02 2.50e+03 5.25e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.564 -0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" CAD G1I R 501 " pdb=" OAK G1I R 501 " ideal model delta sigma weight residual 1.353 1.323 0.030 2.00e-02 2.50e+03 2.29e+00 ... (remaining 2130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 2771 1.18 - 2.35: 128 2.35 - 3.53: 22 3.53 - 4.71: 7 4.71 - 5.88: 6 Bond angle restraints: 2934 Sorted by residual: angle pdb=" C GLU R 180 " pdb=" N ALA R 181 " pdb=" CA ALA R 181 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.48e+00 angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 121.58 116.00 5.58 1.95e+00 2.63e-01 8.20e+00 angle pdb=" N ILE R 135 " pdb=" CA ILE R 135 " pdb=" C ILE R 135 " ideal model delta sigma weight residual 111.00 113.67 -2.67 1.09e+00 8.42e-01 6.01e+00 angle pdb=" C ILE R 135 " pdb=" CA ILE R 135 " pdb=" CB ILE R 135 " ideal model delta sigma weight residual 112.24 109.57 2.67 1.34e+00 5.57e-01 3.98e+00 angle pdb=" N HIS R 296 " pdb=" CA HIS R 296 " pdb=" CB HIS R 296 " ideal model delta sigma weight residual 110.41 113.75 -3.34 1.68e+00 3.54e-01 3.96e+00 ... (remaining 2929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 1094 16.95 - 33.91: 103 33.91 - 50.86: 15 50.86 - 67.82: 0 67.82 - 84.77: 1 Dihedral angle restraints: 1213 sinusoidal: 385 harmonic: 828 Sorted by residual: dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual 93.00 177.77 -84.77 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CA CYS R 190 " pdb=" C CYS R 190 " pdb=" N CYS R 191 " pdb=" CA CYS R 191 " ideal model delta harmonic sigma weight residual 180.00 160.79 19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual 180.00 -162.14 -17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 227 0.033 - 0.066: 90 0.066 - 0.098: 31 0.098 - 0.131: 5 0.131 - 0.164: 1 Chirality restraints: 354 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 2.56 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA ILE R 303 " pdb=" N ILE R 303 " pdb=" C ILE R 303 " pdb=" CB ILE R 303 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA TYR R 219 " pdb=" N TYR R 219 " pdb=" C TYR R 219 " pdb=" CB TYR R 219 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.04e-01 ... (remaining 351 not shown) Planarity restraints: 361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER R 329 " -0.024 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO R 330 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO R 330 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 330 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 173 " -0.011 2.00e-02 2.50e+03 8.68e-03 1.88e+00 pdb=" CG TRP R 173 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP R 173 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 173 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 173 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP R 173 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 173 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 173 " 0.001 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 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO R 168 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.015 5.00e-02 4.00e+02 ... (remaining 358 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 424 2.77 - 3.30: 2103 3.30 - 3.84: 3391 3.84 - 4.37: 3303 4.37 - 4.90: 6123 Nonbonded interactions: 15344 Sorted by model distance: nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.241 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR R 118 " pdb=" OG SER R 161 " model vdw 2.338 3.040 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.449 3.120 nonbonded pdb=" O VAL R 292 " pdb=" ND1 HIS R 296 " model vdw 2.581 3.120 ... (remaining 15339 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.730 Find NCS groups from input model: 0.030 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 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 2135 Z= 0.231 Angle : 0.621 5.882 2934 Z= 0.353 Chirality : 0.040 0.164 354 Planarity : 0.004 0.037 361 Dihedral : 12.729 44.728 669 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: 2.12 (0.50), residues: 277 helix: 2.43 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -1.87 (0.60), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 173 HIS 0.002 0.001 HIS R 178 PHE 0.009 0.001 PHE R 290 TYR 0.014 0.001 TYR R 185 ARG 0.002 0.000 ARG R 175 *********************** 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 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.226 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1395 time to fit residues: 6.6351 Evaluate side-chains 31 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 0.0670 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.156986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.140778 restraints weight = 3252.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143968 restraints weight = 1668.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145913 restraints weight = 1037.167| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2135 Z= 0.156 Angle : 0.524 4.994 2934 Z= 0.291 Chirality : 0.040 0.137 354 Planarity : 0.004 0.032 361 Dihedral : 5.092 18.513 311 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.66 % Allowed : 12.23 % Favored : 85.11 % 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: 2.24 (0.51), residues: 277 helix: 2.39 (0.35), residues: 214 sheet: None (None), residues: 0 loop : -1.89 (0.70), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 173 HIS 0.001 0.001 HIS R 178 PHE 0.007 0.001 PHE R 321 TYR 0.014 0.001 TYR R 185 ARG 0.001 0.000 ARG R 175 *********************** 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 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.255 Fit side-chains REVERT: R 163 LEU cc_start: 0.8101 (mm) cc_final: 0.7807 (tt) REVERT: R 173 TRP cc_start: 0.7027 (m-10) cc_final: 0.6617 (m-90) outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 0.1350 time to fit residues: 5.9406 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.0770 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.0770 chunk 3 optimal weight: 0.6980 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.156297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139360 restraints weight = 3214.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.143570 restraints weight = 1593.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.145667 restraints weight = 870.193| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2135 Z= 0.168 Angle : 0.514 5.165 2934 Z= 0.281 Chirality : 0.040 0.129 354 Planarity : 0.003 0.031 361 Dihedral : 4.723 18.196 311 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.13 % Allowed : 15.43 % Favored : 82.45 % 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: 2.36 (0.51), residues: 277 helix: 2.26 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.48 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.006 0.001 PHE R 217 TYR 0.011 0.001 TYR R 185 ARG 0.002 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.242 Fit side-chains REVERT: R 163 LEU cc_start: 0.7848 (mm) cc_final: 0.7576 (tt) REVERT: R 171 MET cc_start: 0.6864 (ppp) cc_final: 0.6029 (ptm) REVERT: R 173 TRP cc_start: 0.7295 (m-10) cc_final: 0.6860 (m-90) REVERT: R 178 HIS cc_start: 0.8127 (p90) cc_final: 0.7902 (p90) outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 0.1345 time to fit residues: 6.0931 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.150334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.132991 restraints weight = 3278.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137230 restraints weight = 1674.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139154 restraints weight = 905.934| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2135 Z= 0.199 Angle : 0.531 5.526 2934 Z= 0.293 Chirality : 0.041 0.130 354 Planarity : 0.003 0.029 361 Dihedral : 4.697 18.378 311 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.72 % Allowed : 18.09 % Favored : 78.19 % 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: 2.34 (0.51), residues: 277 helix: 2.35 (0.34), residues: 217 sheet: None (None), residues: 0 loop : -1.60 (0.76), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.008 0.001 PHE R 61 TYR 0.009 0.001 TYR R 185 ARG 0.002 0.000 ARG R 175 *********************** 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 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.213 Fit side-chains REVERT: R 163 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7408 (tt) REVERT: R 173 TRP cc_start: 0.7477 (m-10) cc_final: 0.7244 (m-10) REVERT: R 185 TYR cc_start: 0.7166 (m-80) cc_final: 0.6917 (m-80) outliers start: 7 outliers final: 4 residues processed: 35 average time/residue: 0.1407 time to fit residues: 5.9362 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 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 = 0.3693 r_free = 0.3693 target = 0.148568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131180 restraints weight = 3349.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135562 restraints weight = 1703.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.137497 restraints weight = 884.466| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2135 Z= 0.212 Angle : 0.536 5.986 2934 Z= 0.295 Chirality : 0.041 0.130 354 Planarity : 0.003 0.028 361 Dihedral : 4.767 18.675 311 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.72 % Allowed : 18.62 % Favored : 77.66 % 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: 2.24 (0.51), residues: 277 helix: 2.26 (0.34), residues: 218 sheet: None (None), residues: 0 loop : -1.60 (0.77), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.007 0.001 PHE R 61 TYR 0.009 0.001 TYR R 185 ARG 0.002 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.222 Fit side-chains REVERT: R 171 MET cc_start: 0.7047 (ptm) cc_final: 0.6119 (ptm) REVERT: R 173 TRP cc_start: 0.7517 (OUTLIER) cc_final: 0.7144 (m-10) REVERT: R 185 TYR cc_start: 0.7241 (m-80) cc_final: 0.6999 (m-80) outliers start: 7 outliers final: 6 residues processed: 34 average time/residue: 0.1373 time to fit residues: 5.6404 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 173 TRP Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 328 ARG Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 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 = 0.3695 r_free = 0.3695 target = 0.148809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131487 restraints weight = 3349.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.136152 restraints weight = 1743.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.137729 restraints weight = 849.328| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2135 Z= 0.199 Angle : 0.529 6.372 2934 Z= 0.290 Chirality : 0.041 0.129 354 Planarity : 0.003 0.027 361 Dihedral : 4.734 18.603 311 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.26 % Allowed : 20.74 % Favored : 75.00 % 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: 2.27 (0.51), residues: 277 helix: 2.29 (0.34), residues: 218 sheet: None (None), residues: 0 loop : -1.63 (0.77), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.006 0.001 PHE R 61 TYR 0.008 0.001 TYR R 185 ARG 0.002 0.000 ARG R 175 *********************** 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 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.391 Fit side-chains REVERT: R 163 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7364 (tt) REVERT: R 171 MET cc_start: 0.7131 (ptm) cc_final: 0.6101 (ptm) REVERT: R 173 TRP cc_start: 0.7511 (m-10) cc_final: 0.7151 (m-10) outliers start: 8 outliers final: 6 residues processed: 35 average time/residue: 0.1705 time to fit residues: 7.3451 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 328 ARG Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.154523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.138359 restraints weight = 3298.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.141435 restraints weight = 1770.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.143272 restraints weight = 1102.566| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2135 Z= 0.171 Angle : 0.509 5.372 2934 Z= 0.280 Chirality : 0.040 0.126 354 Planarity : 0.003 0.026 361 Dihedral : 4.598 18.317 311 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.72 % Allowed : 20.74 % Favored : 75.53 % 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: 2.44 (0.51), residues: 277 helix: 2.42 (0.34), residues: 218 sheet: None (None), residues: 0 loop : -1.62 (0.78), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.006 0.001 PHE R 193 TYR 0.006 0.001 TYR R 141 ARG 0.002 0.000 ARG R 175 *********************** 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 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.229 Fit side-chains REVERT: R 163 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7469 (tt) REVERT: R 171 MET cc_start: 0.7077 (ptm) cc_final: 0.6276 (ptm) outliers start: 7 outliers final: 4 residues processed: 34 average time/residue: 0.1384 time to fit residues: 5.6285 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 328 ARG Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 5 optimal weight: 0.0970 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.152087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.135773 restraints weight = 3361.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.138828 restraints weight = 1783.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140785 restraints weight = 1132.061| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2135 Z= 0.192 Angle : 0.542 7.050 2934 Z= 0.293 Chirality : 0.040 0.124 354 Planarity : 0.003 0.026 361 Dihedral : 4.699 18.308 311 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.26 % Allowed : 20.21 % Favored : 75.53 % 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: 2.39 (0.50), residues: 277 helix: 2.54 (0.34), residues: 212 sheet: None (None), residues: 0 loop : -1.88 (0.73), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 173 HIS 0.002 0.001 HIS R 172 PHE 0.006 0.001 PHE R 290 TYR 0.008 0.001 TYR R 185 ARG 0.001 0.000 ARG R 175 *********************** 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 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.208 Fit side-chains REVERT: R 171 MET cc_start: 0.6499 (ptm) cc_final: 0.6155 (ppp) outliers start: 8 outliers final: 7 residues processed: 34 average time/residue: 0.1425 time to fit residues: 5.8399 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 328 ARG Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 6 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 12 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 = 0.3722 r_free = 0.3722 target = 0.151341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134862 restraints weight = 3400.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138236 restraints weight = 1774.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139838 restraints weight = 1081.865| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2135 Z= 0.195 Angle : 0.540 6.689 2934 Z= 0.294 Chirality : 0.041 0.125 354 Planarity : 0.003 0.028 361 Dihedral : 4.704 18.327 311 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.79 % Allowed : 20.21 % Favored : 75.00 % 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: 2.34 (0.51), residues: 277 helix: 2.50 (0.34), residues: 212 sheet: None (None), residues: 0 loop : -1.87 (0.74), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.006 0.001 PHE R 217 TYR 0.008 0.001 TYR R 185 ARG 0.002 0.000 ARG R 175 *********************** 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 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.245 Fit side-chains REVERT: R 115 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7443 (tp) REVERT: R 171 MET cc_start: 0.6552 (ptm) cc_final: 0.6293 (ppp) REVERT: R 173 TRP cc_start: 0.7800 (m-10) cc_final: 0.7412 (m-90) outliers start: 9 outliers final: 7 residues processed: 34 average time/residue: 0.1358 time to fit residues: 5.6042 Evaluate side-chains 35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 328 ARG Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.135286 restraints weight = 3277.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.138370 restraints weight = 1756.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.140118 restraints weight = 1115.573| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2135 Z= 0.186 Angle : 0.533 6.542 2934 Z= 0.291 Chirality : 0.040 0.124 354 Planarity : 0.003 0.027 361 Dihedral : 4.676 18.366 311 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.79 % Allowed : 20.21 % Favored : 75.00 % 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: 2.40 (0.51), residues: 277 helix: 2.54 (0.34), residues: 212 sheet: None (None), residues: 0 loop : -1.82 (0.76), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.006 0.001 PHE R 217 TYR 0.007 0.001 TYR R 185 ARG 0.002 0.000 ARG R 175 ********************** 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: 9 poor density : 30 time to evaluate : 0.226 Fit side-chains REVERT: R 115 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7428 (tp) REVERT: R 171 MET cc_start: 0.6478 (ptm) cc_final: 0.5991 (ppp) outliers start: 9 outliers final: 7 residues processed: 36 average time/residue: 0.1383 time to fit residues: 5.9777 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 328 ARG Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 1 optimal weight: 0.4980 chunk 7 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.157933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141440 restraints weight = 3211.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.144569 restraints weight = 1705.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.146428 restraints weight = 1076.236| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2135 Z= 0.154 Angle : 0.514 6.463 2934 Z= 0.282 Chirality : 0.040 0.124 354 Planarity : 0.003 0.025 361 Dihedral : 4.703 21.108 311 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.72 % Allowed : 22.34 % Favored : 73.94 % 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: 2.61 (0.51), residues: 277 helix: 2.68 (0.34), residues: 212 sheet: None (None), residues: 0 loop : -1.73 (0.75), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 313 HIS 0.011 0.003 HIS R 178 PHE 0.006 0.001 PHE R 193 TYR 0.006 0.001 TYR R 185 ARG 0.000 0.000 ARG R 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1128.59 seconds wall clock time: 20 minutes 10.17 seconds (1210.17 seconds total)