Starting phenix.real_space_refine on Wed Mar 5 14:37:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvm_61840/03_2025/9jvm_61840.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvm_61840/03_2025/9jvm_61840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jvm_61840/03_2025/9jvm_61840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvm_61840/03_2025/9jvm_61840.map" model { file = "/net/cci-nas-00/data/ceres_data/9jvm_61840/03_2025/9jvm_61840.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvm_61840/03_2025/9jvm_61840.cif" } resolution = 2.36 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 1183 2.51 5 N 295 2.21 5 O 313 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: 1800 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1800 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 18, 'TRANS': 248} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 180 Time building chain proxies: 3.20, per 1000 atoms: 1.78 Number of scatterers: 1800 At special positions: 0 Unit cell: (70.3, 62.16, 55.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 313 8.00 N 295 7.00 C 1183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 248.2 milliseconds 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 492 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 82.8% 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 14 through 47 Proline residue: R 20 - end of helix removed outlier: 3.586A pdb=" N PHE R 28 " --> pdb=" O TYR R 24 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR R 29 " --> pdb=" O ALA R 25 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU R 30 " --> pdb=" O LEU R 26 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU R 32 " --> pdb=" O PHE R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix removed outlier: 3.520A pdb=" N LEU R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 68 removed outlier: 3.824A pdb=" N LEU R 56 " --> pdb=" O LEU R 52 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS R 68 " --> pdb=" O LEU R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 77 removed outlier: 3.817A pdb=" N TRP R 73 " --> pdb=" O ALA R 69 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP R 75 " --> pdb=" O PRO R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 120 removed outlier: 4.110A pdb=" N ARG R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 129 Processing helix chain 'R' and resid 130 through 148 removed outlier: 3.551A pdb=" N TRP R 142 " --> pdb=" O SER R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 154 removed outlier: 3.506A pdb=" N LEU R 154 " --> pdb=" O PRO R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 191 Processing helix chain 'R' and resid 191 through 210 Processing helix chain 'R' and resid 225 through 227 No H-bonds generated for 'chain 'R' and resid 225 through 227' Processing helix chain 'R' and resid 228 through 253 removed outlier: 4.017A pdb=" N CYS R 232 " --> pdb=" O LEU R 228 " (cutoff:3.500A) Proline residue: R 240 - end of helix removed outlier: 4.038A pdb=" N PHE R 252 " --> pdb=" O ARG R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 294 removed outlier: 4.065A pdb=" N HIS R 276 " --> pdb=" O PHE R 272 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N CYS R 286 " --> pdb=" O ALA R 282 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) Proline residue: R 290 - end of helix Processing helix chain 'R' and resid 296 through 308 removed outlier: 4.453A pdb=" N ALA R 300 " --> pdb=" O ALA R 296 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG R 301 " --> pdb=" O CYS R 297 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 408 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: 0.46 Time building geometry restraints manager: 0.56 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: 474 1.33 - 1.45: 344 1.45 - 1.57: 1013 1.57 - 1.69: 0 1.69 - 1.81: 11 Bond restraints: 1842 Sorted by residual: bond pdb=" CB PHE R 272 " pdb=" CG PHE R 272 " ideal model delta sigma weight residual 1.502 1.464 0.038 2.30e-02 1.89e+03 2.78e+00 bond pdb=" C PHE R 272 " pdb=" N PRO R 273 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.74e+00 bond pdb=" CB VAL R 96 " pdb=" CG1 VAL R 96 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.34e+00 bond pdb=" C LEU R 281 " pdb=" O LEU R 281 " ideal model delta sigma weight residual 1.236 1.253 -0.016 1.15e-02 7.56e+03 2.02e+00 bond pdb=" CB TYR R 55 " pdb=" CG TYR R 55 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.20e-02 2.07e+03 1.91e+00 ... (remaining 1837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 2428 2.43 - 4.86: 91 4.86 - 7.29: 19 7.29 - 9.72: 3 9.72 - 12.15: 1 Bond angle restraints: 2542 Sorted by residual: angle pdb=" CA PRO R 20 " pdb=" N PRO R 20 " pdb=" CD PRO R 20 " ideal model delta sigma weight residual 112.00 106.03 5.97 1.40e+00 5.10e-01 1.82e+01 angle pdb=" CA LEU R 244 " pdb=" CB LEU R 244 " pdb=" CG LEU R 244 " ideal model delta sigma weight residual 116.30 128.45 -12.15 3.50e+00 8.16e-02 1.20e+01 angle pdb=" CA ARG R 207 " pdb=" CB ARG R 207 " pdb=" CG ARG R 207 " ideal model delta sigma weight residual 114.10 121.04 -6.94 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CA PRO R 21 " pdb=" N PRO R 21 " pdb=" CD PRO R 21 " ideal model delta sigma weight residual 112.00 107.22 4.78 1.40e+00 5.10e-01 1.17e+01 angle pdb=" CA PRO R 33 " pdb=" N PRO R 33 " pdb=" CD PRO R 33 " ideal model delta sigma weight residual 112.00 107.25 4.75 1.40e+00 5.10e-01 1.15e+01 ... (remaining 2537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.84: 951 14.84 - 29.67: 89 29.67 - 44.51: 19 44.51 - 59.34: 1 59.34 - 74.18: 2 Dihedral angle restraints: 1062 sinusoidal: 295 harmonic: 767 Sorted by residual: dihedral pdb=" CA PRO R 71 " pdb=" C PRO R 71 " pdb=" N PRO R 72 " pdb=" CA PRO R 72 " ideal model delta harmonic sigma weight residual 180.00 152.11 27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA TYR R 172 " pdb=" C TYR R 172 " pdb=" N PRO R 173 " pdb=" CA PRO R 173 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LEU R 123 " pdb=" C LEU R 123 " pdb=" N ARG R 124 " pdb=" CA ARG R 124 " ideal model delta harmonic sigma weight residual -180.00 -161.27 -18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 1059 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.037: 173 0.037 - 0.074: 93 0.074 - 0.111: 35 0.111 - 0.147: 14 0.147 - 0.184: 2 Chirality restraints: 317 Sorted by residual: chirality pdb=" CG LEU R 66 " pdb=" CB LEU R 66 " pdb=" CD1 LEU R 66 " pdb=" CD2 LEU R 66 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CB ILE R 158 " pdb=" CA ILE R 158 " pdb=" CG1 ILE R 158 " pdb=" CG2 ILE R 158 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA PRO R 72 " pdb=" N PRO R 72 " pdb=" C PRO R 72 " pdb=" CB PRO R 72 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 314 not shown) Planarity restraints: 321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 32 " -0.074 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO R 33 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO R 33 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO R 33 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 19 " -0.069 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO R 20 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO R 20 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO R 20 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 71 " 0.051 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO R 72 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO R 72 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO R 72 " 0.043 5.00e-02 4.00e+02 ... (remaining 318 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 301 2.75 - 3.29: 1823 3.29 - 3.82: 2970 3.82 - 4.36: 3061 4.36 - 4.90: 5332 Nonbonded interactions: 13487 Sorted by model distance: nonbonded pdb=" O ARG R 160 " pdb=" N TYR R 172 " model vdw 2.211 3.120 nonbonded pdb=" O ASP R 75 " pdb=" N ARG R 79 " model vdw 2.285 3.120 nonbonded pdb=" O HIS R 165 " pdb=" NE2 HIS R 276 " model vdw 2.361 3.120 nonbonded pdb=" OH TYR R 238 " pdb=" OD1 ASN R 285 " model vdw 2.493 3.040 nonbonded pdb=" O TRP R 43 " pdb=" N VAL R 46 " model vdw 2.496 3.120 ... (remaining 13482 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 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: 3.690 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.780 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 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 : 0.009 0.064 1842 Z= 0.569 Angle : 1.113 12.147 2542 Z= 0.570 Chirality : 0.054 0.184 317 Planarity : 0.012 0.111 321 Dihedral : 12.646 74.178 570 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.20 % Favored : 88.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.51), residues: 259 helix: 0.05 (0.36), residues: 187 sheet: None (None), residues: 0 loop : -4.48 (0.62), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 142 HIS 0.007 0.003 HIS R 242 PHE 0.023 0.003 PHE R 272 TYR 0.017 0.002 TYR R 85 ARG 0.015 0.002 ARG R 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.170 Fit side-chains REVERT: R 77 TYR cc_start: 0.5003 (t80) cc_final: 0.4730 (t80) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.5857 time to fit residues: 15.3046 Evaluate side-chains 24 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.0980 chunk 19 optimal weight: 0.0770 chunk 10 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 0.0970 chunk 23 optimal weight: 0.0270 chunk 16 optimal weight: 0.3980 overall best weight: 0.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.193050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.182868 restraints weight = 3155.219| |-----------------------------------------------------------------------------| r_work (start): 0.4540 rms_B_bonded: 1.87 r_work: 0.4481 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4383 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 1842 Z= 0.225 Angle : 0.806 7.547 2542 Z= 0.386 Chirality : 0.040 0.123 317 Planarity : 0.010 0.072 321 Dihedral : 5.024 20.234 279 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.00 % Allowed : 12.67 % Favored : 85.33 % 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: -0.03 (0.53), residues: 259 helix: 1.32 (0.38), residues: 188 sheet: None (None), residues: 0 loop : -3.89 (0.60), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 43 HIS 0.003 0.001 HIS R 276 PHE 0.004 0.001 PHE R 95 TYR 0.021 0.001 TYR R 169 ARG 0.001 0.000 ARG R 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.181 Fit side-chains REVERT: R 244 LEU cc_start: 0.3947 (tp) cc_final: 0.3356 (tp) outliers start: 3 outliers final: 1 residues processed: 25 average time/residue: 0.5269 time to fit residues: 13.7870 Evaluate side-chains 25 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 16 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.188918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.178326 restraints weight = 3085.846| |-----------------------------------------------------------------------------| r_work (start): 0.4498 rms_B_bonded: 1.94 r_work: 0.4434 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4331 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 1842 Z= 0.313 Angle : 0.807 6.395 2542 Z= 0.403 Chirality : 0.043 0.130 317 Planarity : 0.010 0.066 321 Dihedral : 5.147 21.945 279 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.67 % Allowed : 14.67 % Favored : 82.67 % 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: 0.05 (0.54), residues: 259 helix: 1.34 (0.38), residues: 189 sheet: None (None), residues: 0 loop : -3.83 (0.62), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP R 43 HIS 0.004 0.001 HIS R 242 PHE 0.012 0.001 PHE R 272 TYR 0.011 0.001 TYR R 98 ARG 0.002 0.000 ARG R 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.186 Fit side-chains REVERT: R 244 LEU cc_start: 0.4090 (tp) cc_final: 0.3147 (mt) outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 0.5031 time to fit residues: 13.2285 Evaluate side-chains 25 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 0.0010 chunk 13 optimal weight: 0.4980 chunk 3 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.0970 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.1982 ------------------------------------------------------------------------------- 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 = 0.4661 r_free = 0.4661 target = 0.193215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.182897 restraints weight = 3085.129| |-----------------------------------------------------------------------------| r_work (start): 0.4548 rms_B_bonded: 1.90 r_work: 0.4487 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4388 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 1842 Z= 0.232 Angle : 0.746 6.886 2542 Z= 0.359 Chirality : 0.040 0.124 317 Planarity : 0.009 0.059 321 Dihedral : 4.638 19.292 279 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.67 % Allowed : 17.33 % Favored : 80.00 % 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: 0.43 (0.54), residues: 259 helix: 1.60 (0.39), residues: 190 sheet: None (None), residues: 0 loop : -3.71 (0.59), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 43 HIS 0.003 0.001 HIS R 242 PHE 0.005 0.001 PHE R 95 TYR 0.008 0.001 TYR R 98 ARG 0.001 0.000 ARG R 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.182 Fit side-chains REVERT: R 66 LEU cc_start: 0.7124 (mm) cc_final: 0.6873 (mm) REVERT: R 244 LEU cc_start: 0.3909 (tp) cc_final: 0.2930 (mt) outliers start: 4 outliers final: 1 residues processed: 25 average time/residue: 0.4934 time to fit residues: 13.0047 Evaluate side-chains 23 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 6 optimal weight: 0.0870 chunk 9 optimal weight: 0.2980 chunk 21 optimal weight: 0.3980 chunk 24 optimal weight: 0.4980 chunk 3 optimal weight: 0.1980 overall best weight: 0.2158 ------------------------------------------------------------------------------- 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 = 0.4657 r_free = 0.4657 target = 0.192672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.182302 restraints weight = 3222.205| |-----------------------------------------------------------------------------| r_work (start): 0.4541 rms_B_bonded: 1.98 r_work: 0.4476 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 1842 Z= 0.236 Angle : 0.757 9.710 2542 Z= 0.357 Chirality : 0.040 0.125 317 Planarity : 0.008 0.056 321 Dihedral : 4.517 18.814 279 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.00 % Allowed : 22.67 % Favored : 75.33 % 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: 0.77 (0.55), residues: 259 helix: 1.69 (0.39), residues: 192 sheet: None (None), residues: 0 loop : -3.18 (0.67), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 43 HIS 0.003 0.001 HIS R 242 PHE 0.006 0.001 PHE R 95 TYR 0.008 0.001 TYR R 98 ARG 0.001 0.000 ARG R 248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.225 Fit side-chains REVERT: R 244 LEU cc_start: 0.3553 (tp) cc_final: 0.2940 (mt) outliers start: 3 outliers final: 1 residues processed: 25 average time/residue: 0.7442 time to fit residues: 19.6091 Evaluate side-chains 23 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 11 optimal weight: 0.0570 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 0.0870 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 overall best weight: 0.1654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.193014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.182895 restraints weight = 3228.313| |-----------------------------------------------------------------------------| r_work (start): 0.4546 rms_B_bonded: 1.92 r_work: 0.4486 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4389 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 1842 Z= 0.223 Angle : 0.756 10.667 2542 Z= 0.351 Chirality : 0.040 0.135 317 Planarity : 0.008 0.054 321 Dihedral : 4.345 17.782 279 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.33 % Allowed : 26.67 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.55), residues: 259 helix: 1.86 (0.39), residues: 189 sheet: None (None), residues: 0 loop : -2.68 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 43 HIS 0.002 0.001 HIS R 242 PHE 0.005 0.001 PHE R 95 TYR 0.006 0.001 TYR R 98 ARG 0.000 0.000 ARG R 248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.176 Fit side-chains REVERT: R 244 LEU cc_start: 0.3928 (tp) cc_final: 0.3028 (mt) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.5295 time to fit residues: 13.3971 Evaluate side-chains 24 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 8 optimal weight: 0.2980 chunk 11 optimal weight: 0.0170 chunk 10 optimal weight: 0.0770 chunk 12 optimal weight: 0.0980 chunk 1 optimal weight: 0.0670 chunk 19 optimal weight: 0.4980 chunk 2 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.0914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.196423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.186119 restraints weight = 3248.280| |-----------------------------------------------------------------------------| r_work (start): 0.4575 rms_B_bonded: 1.96 r_work: 0.4517 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4416 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1842 Z= 0.213 Angle : 0.759 9.643 2542 Z= 0.342 Chirality : 0.039 0.127 317 Planarity : 0.008 0.053 321 Dihedral : 4.024 16.789 279 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.33 % Allowed : 27.33 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.56), residues: 259 helix: 1.88 (0.39), residues: 192 sheet: None (None), residues: 0 loop : -2.86 (0.71), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 43 HIS 0.002 0.001 HIS R 242 PHE 0.005 0.001 PHE R 95 TYR 0.004 0.001 TYR R 98 ARG 0.000 0.000 ARG R 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.183 Fit side-chains REVERT: R 244 LEU cc_start: 0.3729 (tp) cc_final: 0.2835 (mt) outliers start: 2 outliers final: 1 residues processed: 23 average time/residue: 0.5431 time to fit residues: 13.1491 Evaluate side-chains 24 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 0.0570 chunk 21 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.0040 chunk 20 optimal weight: 0.4980 chunk 8 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.0970 chunk 17 optimal weight: 0.0870 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 overall best weight: 0.0686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.197383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.186994 restraints weight = 3325.518| |-----------------------------------------------------------------------------| r_work (start): 0.4586 rms_B_bonded: 2.03 r_work: 0.4527 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work (final): 0.4527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1842 Z= 0.223 Angle : 0.776 8.946 2542 Z= 0.354 Chirality : 0.039 0.127 317 Planarity : 0.008 0.052 321 Dihedral : 3.930 16.914 279 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 29.33 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.56), residues: 259 helix: 1.91 (0.39), residues: 192 sheet: None (None), residues: 0 loop : -2.84 (0.72), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 43 HIS 0.002 0.001 HIS R 242 PHE 0.005 0.001 PHE R 95 TYR 0.011 0.001 TYR R 238 ARG 0.005 0.001 ARG R 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.186 Fit side-chains REVERT: R 244 LEU cc_start: 0.3333 (tp) cc_final: 0.2831 (mt) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.5754 time to fit residues: 14.0893 Evaluate side-chains 22 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 0.2980 chunk 2 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.0040 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 23 optimal weight: 0.0270 chunk 11 optimal weight: 0.0040 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 overall best weight: 0.1462 ------------------------------------------------------------------------------- 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 = 0.4666 r_free = 0.4666 target = 0.194928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.184527 restraints weight = 3254.386| |-----------------------------------------------------------------------------| r_work (start): 0.4556 rms_B_bonded: 1.98 r_work: 0.4496 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4398 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1842 Z= 0.221 Angle : 0.757 9.306 2542 Z= 0.344 Chirality : 0.040 0.126 317 Planarity : 0.009 0.090 321 Dihedral : 3.930 16.128 279 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.67 % Allowed : 28.00 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.56), residues: 259 helix: 2.04 (0.39), residues: 188 sheet: None (None), residues: 0 loop : -2.44 (0.74), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 40 HIS 0.002 0.001 HIS R 242 PHE 0.005 0.001 PHE R 95 TYR 0.014 0.001 TYR R 238 ARG 0.001 0.000 ARG R 248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.207 Fit side-chains REVERT: R 244 LEU cc_start: 0.3769 (tp) cc_final: 0.2964 (mt) outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.5710 time to fit residues: 15.0494 Evaluate side-chains 22 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.0010 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.0770 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.3144 ------------------------------------------------------------------------------- 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 = 0.4623 r_free = 0.4623 target = 0.190809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.180211 restraints weight = 3332.216| |-----------------------------------------------------------------------------| r_work (start): 0.4510 rms_B_bonded: 2.06 r_work: 0.4448 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 1842 Z= 0.268 Angle : 0.813 11.546 2542 Z= 0.377 Chirality : 0.043 0.143 317 Planarity : 0.009 0.081 321 Dihedral : 4.364 18.757 279 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 30.00 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.55), residues: 259 helix: 1.90 (0.39), residues: 186 sheet: None (None), residues: 0 loop : -2.68 (0.71), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 40 HIS 0.003 0.001 HIS R 242 PHE 0.006 0.001 PHE R 272 TYR 0.009 0.001 TYR R 98 ARG 0.002 0.001 ARG R 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.189 Fit side-chains REVERT: R 244 LEU cc_start: 0.3726 (tp) cc_final: 0.3315 (mt) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.5786 time to fit residues: 14.0321 Evaluate side-chains 23 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 0.0030 chunk 3 optimal weight: 0.0010 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.0770 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.0980 chunk 11 optimal weight: 0.1980 chunk 1 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 overall best weight: 0.0754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.197290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.186500 restraints weight = 3209.841| |-----------------------------------------------------------------------------| r_work (start): 0.4580 rms_B_bonded: 2.05 r_work: 0.4521 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1842 Z= 0.217 Angle : 0.797 11.922 2542 Z= 0.355 Chirality : 0.039 0.114 317 Planarity : 0.008 0.069 321 Dihedral : 3.963 15.837 279 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 30.00 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.56), residues: 259 helix: 2.09 (0.39), residues: 188 sheet: None (None), residues: 0 loop : -2.37 (0.74), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 43 HIS 0.002 0.001 HIS R 242 PHE 0.005 0.001 PHE R 95 TYR 0.013 0.001 TYR R 238 ARG 0.000 0.000 ARG R 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2211.57 seconds wall clock time: 38 minutes 34.58 seconds (2314.58 seconds total)