Starting phenix.real_space_refine on Wed Mar 5 14:50:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggo_40015/03_2025/8ggo_40015.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggo_40015/03_2025/8ggo_40015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggo_40015/03_2025/8ggo_40015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggo_40015/03_2025/8ggo_40015.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggo_40015/03_2025/8ggo_40015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggo_40015/03_2025/8ggo_40015.cif" } resolution = 3.2 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 13 5.16 5 C 1403 2.51 5 N 330 2.21 5 O 349 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-5624/modules/chem_data/mon_lib" Total number of atoms: 2095 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2080 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 7, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 92 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: 2.47, per 1000 atoms: 1.18 Number of scatterers: 2095 At special positions: 0 Unit cell: (56.4005, 82.4315, 64.2098, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 13 16.00 O 349 8.00 N 330 7.00 C 1403 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=2.04 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: 0.61 Conformation dependent library (CDL) restraints added in 295.1 milliseconds 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 534 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 89.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'R' and resid 37 through 61 removed outlier: 3.566A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 66 removed outlier: 3.587A pdb=" N GLN R 65 " --> pdb=" O GLU R 62 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR R 66 " --> pdb=" O ARG R 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 62 through 66' Processing helix chain 'R' and resid 67 through 86 removed outlier: 4.311A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 removed outlier: 3.534A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.690A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.844A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix 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 270 through 299 removed outlier: 3.741A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.524A pdb=" N ILE R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.627A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 326 removed outlier: 3.819A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 removed outlier: 3.649A pdb=" N GLU R 338 " --> pdb=" O ILE R 334 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU R 340 " --> pdb=" O PHE R 336 " (cutoff:3.500A) 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: 0.52 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 359 1.33 - 1.45: 594 1.45 - 1.57: 1180 1.57 - 1.69: 1 1.69 - 1.81: 17 Bond restraints: 2151 Sorted by residual: bond pdb=" C ARG R 328 " pdb=" N SER R 329 " ideal model delta sigma weight residual 1.331 1.250 0.081 2.07e-02 2.33e+03 1.51e+01 bond pdb=" C CYS R 327 " pdb=" N ARG R 328 " ideal model delta sigma weight residual 1.332 1.284 0.048 1.37e-02 5.33e+03 1.23e+01 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" CA VAL R 86 " pdb=" C VAL R 86 " ideal model delta sigma weight residual 1.523 1.487 0.036 1.37e-02 5.33e+03 6.77e+00 bond pdb=" CA VAL R 81 " pdb=" C VAL R 81 " ideal model delta sigma weight residual 1.523 1.493 0.031 1.27e-02 6.20e+03 5.77e+00 ... (remaining 2146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 2879 1.85 - 3.71: 55 3.71 - 5.56: 16 5.56 - 7.42: 5 7.42 - 9.27: 2 Bond angle restraints: 2957 Sorted by residual: angle pdb=" N LEU R 84 " pdb=" CA LEU R 84 " pdb=" C LEU R 84 " ideal model delta sigma weight residual 111.36 118.41 -7.05 1.09e+00 8.42e-01 4.18e+01 angle pdb=" N ALA R 85 " pdb=" CA ALA R 85 " pdb=" C ALA R 85 " ideal model delta sigma weight residual 113.97 122.12 -8.15 1.28e+00 6.10e-01 4.05e+01 angle pdb=" N CYS R 327 " pdb=" CA CYS R 327 " pdb=" C CYS R 327 " ideal model delta sigma weight residual 111.07 116.65 -5.58 1.07e+00 8.73e-01 2.72e+01 angle pdb=" N TYR R 326 " pdb=" CA TYR R 326 " pdb=" C TYR R 326 " ideal model delta sigma weight residual 111.69 118.05 -6.36 1.23e+00 6.61e-01 2.67e+01 angle pdb=" C VAL R 87 " pdb=" N PRO R 88 " pdb=" CA PRO R 88 " ideal model delta sigma weight residual 119.05 113.44 5.61 1.11e+00 8.12e-01 2.55e+01 ... (remaining 2952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 1102 14.89 - 29.77: 89 29.77 - 44.65: 25 44.65 - 59.53: 2 59.53 - 74.41: 1 Dihedral angle restraints: 1219 sinusoidal: 397 harmonic: 822 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 -86.00 -160.41 74.41 1 1.00e+01 1.00e-02 7.02e+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 -163.62 -16.38 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA SER R 207 " pdb=" C SER R 207 " pdb=" N PHE R 208 " pdb=" CA PHE R 208 " ideal model delta harmonic sigma weight residual -180.00 -163.74 -16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 1216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 280 0.048 - 0.096: 71 0.096 - 0.144: 11 0.144 - 0.191: 4 0.191 - 0.239: 2 Chirality restraints: 368 Sorted by residual: chirality pdb=" CA ALA R 85 " pdb=" N ALA R 85 " pdb=" C ALA R 85 " pdb=" CB ALA R 85 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA PHE R 89 " pdb=" N PHE R 89 " pdb=" C PHE R 89 " pdb=" CB PHE R 89 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA CYS R 327 " pdb=" N CYS R 327 " pdb=" C CYS R 327 " pdb=" CB CYS R 327 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 365 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS R 327 " 0.016 2.00e-02 2.50e+03 3.05e-02 9.28e+00 pdb=" C CYS R 327 " -0.053 2.00e-02 2.50e+03 pdb=" O CYS R 327 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG R 328 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 79 " 0.009 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C ASP R 79 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP R 79 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU R 80 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 328 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.89e+00 pdb=" C ARG R 328 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG R 328 " -0.009 2.00e-02 2.50e+03 pdb=" N SER R 329 " -0.008 2.00e-02 2.50e+03 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 610 2.83 - 3.34: 2140 3.34 - 3.86: 3322 3.86 - 4.38: 3474 4.38 - 4.90: 6381 Nonbonded interactions: 15927 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.307 3.040 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.353 3.120 nonbonded pdb=" OD2 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.452 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAK G1I R 501 " model vdw 2.489 3.040 nonbonded pdb=" O ALA R 119 " pdb=" OG1 THR R 123 " model vdw 2.532 3.040 ... (remaining 15922 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.005 0.081 2151 Z= 0.360 Angle : 0.737 9.272 2957 Z= 0.481 Chirality : 0.046 0.239 368 Planarity : 0.004 0.030 354 Dihedral : 11.582 49.341 682 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 2.30 (0.50), residues: 275 helix: 2.14 (0.34), residues: 218 sheet: None (None), residues: 0 loop : -0.93 (0.81), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.010 0.001 PHE R 89 TYR 0.010 0.001 TYR R 132 ARG 0.001 0.000 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.215 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1670 time to fit residues: 2.9688 Evaluate side-chains 11 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.135779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.120835 restraints weight = 2874.815| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.83 r_work: 0.3252 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2151 Z= 0.204 Angle : 0.493 5.213 2957 Z= 0.278 Chirality : 0.040 0.116 368 Planarity : 0.004 0.027 354 Dihedral : 4.628 19.872 308 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.97 % Allowed : 2.96 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.41 (0.51), residues: 275 helix: 2.21 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.13 (0.78), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 PHE 0.011 0.001 PHE R 108 TYR 0.010 0.001 TYR R 199 ARG 0.002 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.227 Fit side-chains REVERT: R 82 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7292 (mtm) outliers start: 4 outliers final: 1 residues processed: 15 average time/residue: 0.0700 time to fit residues: 1.6856 Evaluate side-chains 13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.135147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120510 restraints weight = 2829.807| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.71 r_work: 0.3241 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2151 Z= 0.196 Angle : 0.475 5.283 2957 Z= 0.267 Chirality : 0.039 0.117 368 Planarity : 0.003 0.026 354 Dihedral : 4.399 19.831 308 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.97 % Allowed : 4.43 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.49 (0.51), residues: 275 helix: 2.25 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.00 (0.81), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.008 0.001 PHE R 108 TYR 0.009 0.001 TYR R 199 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.232 Fit side-chains REVERT: R 82 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7433 (mtm) outliers start: 4 outliers final: 1 residues processed: 15 average time/residue: 0.0779 time to fit residues: 1.8168 Evaluate side-chains 12 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 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 = 0.3479 r_free = 0.3479 target = 0.132903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.118286 restraints weight = 2839.999| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.67 r_work: 0.3222 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.003 0.029 2151 Z= 0.225 Angle : 0.486 5.267 2957 Z= 0.275 Chirality : 0.040 0.116 368 Planarity : 0.004 0.027 354 Dihedral : 4.460 20.652 308 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.97 % Allowed : 7.88 % Favored : 90.15 % 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: 2.41 (0.52), residues: 275 helix: 2.18 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -0.96 (0.84), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.009 0.001 PHE R 61 TYR 0.011 0.001 TYR R 199 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 11 time to evaluate : 0.205 Fit side-chains REVERT: R 82 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7471 (mtm) outliers start: 4 outliers final: 2 residues processed: 14 average time/residue: 0.0692 time to fit residues: 1.5944 Evaluate side-chains 14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 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 = 0.3479 r_free = 0.3479 target = 0.132900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.118249 restraints weight = 2892.951| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.68 r_work: 0.3231 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2151 Z= 0.213 Angle : 0.470 5.290 2957 Z= 0.266 Chirality : 0.039 0.114 368 Planarity : 0.003 0.028 354 Dihedral : 4.409 20.729 308 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.48 % Allowed : 10.84 % Favored : 87.68 % 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: 2.42 (0.52), residues: 275 helix: 2.20 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.04 (0.83), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.008 0.001 PHE R 61 TYR 0.010 0.001 TYR R 199 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.235 Fit side-chains REVERT: R 82 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7483 (mtm) outliers start: 3 outliers final: 2 residues processed: 13 average time/residue: 0.0690 time to fit residues: 1.4909 Evaluate side-chains 14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 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 = 0.3449 r_free = 0.3449 target = 0.130635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.116300 restraints weight = 2864.680| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.64 r_work: 0.3229 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2151 Z= 0.213 Angle : 0.470 5.260 2957 Z= 0.266 Chirality : 0.039 0.115 368 Planarity : 0.003 0.028 354 Dihedral : 4.384 20.814 308 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.48 % Allowed : 11.82 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.41 (0.52), residues: 275 helix: 2.21 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.15 (0.83), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.009 0.001 PHE R 61 TYR 0.010 0.001 TYR R 199 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.221 Fit side-chains REVERT: R 82 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7500 (mtm) outliers start: 3 outliers final: 2 residues processed: 13 average time/residue: 0.0696 time to fit residues: 1.4975 Evaluate side-chains 14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.130443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.115506 restraints weight = 2869.617| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.80 r_work: 0.3194 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2151 Z= 0.227 Angle : 0.477 5.276 2957 Z= 0.270 Chirality : 0.039 0.115 368 Planarity : 0.003 0.028 354 Dihedral : 4.423 20.830 308 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.48 % Allowed : 12.81 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.33 (0.52), residues: 275 helix: 2.16 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.18 (0.82), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.009 0.001 PHE R 61 TYR 0.010 0.001 TYR R 199 ARG 0.001 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.223 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 13 average time/residue: 0.0699 time to fit residues: 1.5053 Evaluate side-chains 13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.0020 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.0060 overall best weight: 0.3402 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.135898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.120879 restraints weight = 2895.979| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.82 r_work: 0.3274 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2151 Z= 0.144 Angle : 0.431 5.213 2957 Z= 0.242 Chirality : 0.038 0.112 368 Planarity : 0.003 0.028 354 Dihedral : 4.192 21.164 308 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.99 % Allowed : 13.30 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.60 (0.52), residues: 275 helix: 2.36 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.17 (0.82), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.006 0.001 PHE R 61 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.238 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 14 average time/residue: 0.0696 time to fit residues: 1.5760 Evaluate side-chains 13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.134434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119607 restraints weight = 2895.618| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.80 r_work: 0.3258 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2151 Z= 0.165 Angle : 0.440 5.227 2957 Z= 0.247 Chirality : 0.038 0.111 368 Planarity : 0.003 0.028 354 Dihedral : 4.167 20.750 308 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.48 % Allowed : 13.30 % Favored : 85.22 % 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: 2.60 (0.52), residues: 275 helix: 2.35 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.09 (0.82), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.007 0.001 PHE R 61 TYR 0.009 0.001 TYR R 199 ARG 0.001 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.228 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 14 average time/residue: 0.0708 time to fit residues: 1.6052 Evaluate side-chains 14 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 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 = 0.3474 r_free = 0.3474 target = 0.132813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.118232 restraints weight = 2875.836| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.66 r_work: 0.3205 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2151 Z= 0.228 Angle : 0.477 5.261 2957 Z= 0.269 Chirality : 0.040 0.115 368 Planarity : 0.003 0.029 354 Dihedral : 4.360 20.523 308 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.48 % Allowed : 13.30 % Favored : 85.22 % 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: 2.43 (0.52), residues: 275 helix: 2.23 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.15 (0.82), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 313 HIS 0.004 0.001 HIS R 296 PHE 0.009 0.001 PHE R 61 TYR 0.011 0.001 TYR R 199 ARG 0.001 0.000 ARG R 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.225 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 13 average time/residue: 0.0687 time to fit residues: 1.4952 Evaluate side-chains 13 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 0.0000 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.132290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.117228 restraints weight = 2888.021| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.82 r_work: 0.3230 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2151 Z= 0.188 Angle : 0.453 5.247 2957 Z= 0.255 Chirality : 0.039 0.115 368 Planarity : 0.003 0.028 354 Dihedral : 4.262 20.931 308 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.48 % Allowed : 13.79 % Favored : 84.73 % 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: 2.47 (0.52), residues: 275 helix: 2.27 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.21 (0.81), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 99 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 61 TYR 0.009 0.001 TYR R 199 ARG 0.001 0.000 ARG R 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1479.82 seconds wall clock time: 26 minutes 5.18 seconds (1565.18 seconds total)