Starting phenix.real_space_refine on Mon Feb 10 20:05:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggr_40018/02_2025/8ggr_40018.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggr_40018/02_2025/8ggr_40018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggr_40018/02_2025/8ggr_40018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggr_40018/02_2025/8ggr_40018.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggr_40018/02_2025/8ggr_40018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggr_40018/02_2025/8ggr_40018.cif" } resolution = 3.4 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 1434 2.51 5 N 335 2.21 5 O 358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2143 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2127 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 90 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.31, per 1000 atoms: 1.08 Number of scatterers: 2143 At special positions: 0 Unit cell: (55.5328, 85.0346, 62.4744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 358 8.00 N 335 7.00 C 1434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 274.7 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 89.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.779A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET R 40 " --> pdb=" O MET R 36 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 68 through 97 removed outlier: 3.998A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.505A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 removed outlier: 3.502A pdb=" N LEU R 145 " --> pdb=" O TYR R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.508A pdb=" N ALA R 150 " --> pdb=" O THR R 146 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.635A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) 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: 4.078A pdb=" N THR R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.616A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.810A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 327 removed outlier: 3.652A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.650A 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 340 163 hydrogen bonds defined for protein. 486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.54 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 633 1.35 - 1.46: 570 1.46 - 1.58: 972 1.58 - 1.70: 0 1.70 - 1.81: 23 Bond restraints: 2198 Sorted by residual: 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 6.91e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.572 -0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.565 -0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.438 -0.044 2.00e-02 2.50e+03 4.91e+00 bond pdb=" CAD G1I R 501 " pdb=" OAK G1I R 501 " ideal model delta sigma weight residual 1.353 1.322 0.031 2.00e-02 2.50e+03 2.38e+00 ... (remaining 2193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 2901 1.12 - 2.24: 82 2.24 - 3.36: 19 3.36 - 4.48: 4 4.48 - 5.60: 7 Bond angle restraints: 3013 Sorted by residual: angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 116.49 -5.60 3.00e+00 1.11e-01 3.49e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.21 -5.58 3.00e+00 1.11e-01 3.46e+00 angle pdb=" N ILE R 94 " pdb=" CA ILE R 94 " pdb=" CB ILE R 94 " ideal model delta sigma weight residual 110.57 112.94 -2.37 1.28e+00 6.10e-01 3.42e+00 angle pdb=" CB MET R 279 " pdb=" CG MET R 279 " pdb=" SD MET R 279 " ideal model delta sigma weight residual 112.70 117.41 -4.71 3.00e+00 1.11e-01 2.46e+00 angle pdb=" C SER R 207 " pdb=" N PHE R 208 " pdb=" CA PHE R 208 " ideal model delta sigma weight residual 122.46 119.69 2.77 1.80e+00 3.09e-01 2.37e+00 ... (remaining 3008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 1129 17.06 - 34.12: 105 34.12 - 51.18: 20 51.18 - 68.24: 0 68.24 - 85.30: 3 Dihedral angle restraints: 1257 sinusoidal: 429 harmonic: 828 Sorted by residual: dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual -86.00 -171.30 85.30 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CA TYR R 174 " pdb=" C TYR R 174 " pdb=" N ARG R 175 " pdb=" CA ARG R 175 " ideal model delta harmonic sigma weight residual -180.00 -162.22 -17.78 0 5.00e+00 4.00e-02 1.26e+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 -163.84 -16.16 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 1254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 218 0.029 - 0.058: 102 0.058 - 0.087: 36 0.087 - 0.116: 14 0.116 - 0.145: 2 Chirality restraints: 372 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.54 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA PRO R 138 " pdb=" N PRO R 138 " pdb=" C PRO R 138 " pdb=" CB PRO R 138 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA PRO R 288 " pdb=" N PRO R 288 " pdb=" C PRO R 288 " pdb=" CB PRO R 288 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.98e-01 ... (remaining 369 not shown) Planarity restraints: 359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO R 168 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 173 " -0.010 2.00e-02 2.50e+03 6.01e-03 9.03e-01 pdb=" CG TRP R 173 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP R 173 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP R 173 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 173 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 173 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 173 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 173 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 173 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 174 " -0.005 2.00e-02 2.50e+03 6.69e-03 8.96e-01 pdb=" CG TYR R 174 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR R 174 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR R 174 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR R 174 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR R 174 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR R 174 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 174 " 0.001 2.00e-02 2.50e+03 ... (remaining 356 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 822 2.89 - 3.39: 2198 3.39 - 3.89: 3321 3.89 - 4.40: 3453 4.40 - 4.90: 6239 Nonbonded interactions: 16033 Sorted by model distance: nonbonded pdb=" OH TYR R 185 " pdb=" O PHE R 194 " model vdw 2.387 3.040 nonbonded pdb=" OD1 ASN R 196 " pdb=" N GLN R 197 " model vdw 2.475 3.120 nonbonded pdb=" OG SER R 120 " pdb=" O HOH R 601 " model vdw 2.519 3.040 nonbonded pdb=" OE1 GLU R 107 " pdb=" OH TYR R 174 " model vdw 2.524 3.040 nonbonded pdb=" O THR R 189 " pdb=" OG1 THR R 189 " model vdw 2.525 3.040 ... (remaining 16028 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: 1.460 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: 0.020 Set scattering table: 0.030 Process input model: 10.690 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 2198 Z= 0.255 Angle : 0.543 5.602 3013 Z= 0.287 Chirality : 0.040 0.145 372 Planarity : 0.004 0.038 359 Dihedral : 13.102 72.445 716 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 1.94 (0.51), residues: 277 helix: 2.21 (0.35), residues: 212 sheet: None (None), residues: 0 loop : -2.00 (0.65), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.014 0.001 PHE R 139 TYR 0.016 0.001 TYR R 174 ARG 0.005 0.001 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.241 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2003 time to fit residues: 6.4688 Evaluate side-chains 24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116853 restraints weight = 3022.954| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.73 r_work: 0.3229 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2198 Z= 0.177 Angle : 0.468 5.150 3013 Z= 0.259 Chirality : 0.038 0.115 372 Planarity : 0.003 0.032 359 Dihedral : 4.179 16.730 310 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.70 % Allowed : 6.48 % Favored : 89.81 % 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: 2.35 (0.52), residues: 277 helix: 2.31 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -1.75 (0.79), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 173 HIS 0.003 0.001 HIS R 178 PHE 0.010 0.001 PHE R 282 TYR 0.006 0.001 TYR R 308 ARG 0.002 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.237 Fit side-chains REVERT: R 334 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8081 (mp) outliers start: 8 outliers final: 4 residues processed: 31 average time/residue: 0.1831 time to fit residues: 6.6042 Evaluate side-chains 28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain R residue 340 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.132694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117629 restraints weight = 2974.135| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.75 r_work: 0.3251 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2198 Z= 0.175 Angle : 0.463 5.125 3013 Z= 0.256 Chirality : 0.038 0.112 372 Planarity : 0.003 0.026 359 Dihedral : 4.174 16.744 310 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.24 % Allowed : 12.96 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.51), residues: 277 helix: 2.39 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.82 (0.80), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 173 HIS 0.005 0.002 HIS R 178 PHE 0.011 0.001 PHE R 282 TYR 0.006 0.001 TYR R 308 ARG 0.003 0.001 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: R 334 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8102 (mp) outliers start: 7 outliers final: 3 residues processed: 28 average time/residue: 0.1879 time to fit residues: 6.1185 Evaluate side-chains 26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 334 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.116048 restraints weight = 3049.807| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.72 r_work: 0.3211 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2198 Z= 0.174 Angle : 0.455 5.115 3013 Z= 0.252 Chirality : 0.038 0.111 372 Planarity : 0.003 0.027 359 Dihedral : 4.137 16.708 310 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.85 % Allowed : 15.74 % Favored : 82.41 % 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: 2.51 (0.51), residues: 277 helix: 2.46 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.89 (0.79), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 173 HIS 0.003 0.001 HIS R 93 PHE 0.010 0.001 PHE R 282 TYR 0.006 0.001 TYR R 308 ARG 0.004 0.001 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.253 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.2222 time to fit residues: 6.5016 Evaluate side-chains 24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.127476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113312 restraints weight = 3099.062| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.73 r_work: 0.3183 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2198 Z= 0.208 Angle : 0.480 5.166 3013 Z= 0.265 Chirality : 0.039 0.111 372 Planarity : 0.003 0.027 359 Dihedral : 4.203 16.677 310 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.78 % Allowed : 15.74 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.51), residues: 277 helix: 2.38 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.92 (0.79), residues: 55 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 0.011 0.001 PHE R 282 TYR 0.007 0.001 TYR R 308 ARG 0.005 0.001 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: R 72 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7771 (mp) outliers start: 6 outliers final: 3 residues processed: 26 average time/residue: 0.2018 time to fit residues: 6.1027 Evaluate side-chains 25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.128800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.114692 restraints weight = 3086.476| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.71 r_work: 0.3194 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2198 Z= 0.181 Angle : 0.459 5.130 3013 Z= 0.253 Chirality : 0.038 0.109 372 Planarity : 0.003 0.026 359 Dihedral : 4.147 16.710 310 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.85 % Allowed : 17.59 % Favored : 80.56 % 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: 2.51 (0.51), residues: 277 helix: 2.45 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.84 (0.80), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 99 HIS 0.002 0.001 HIS R 296 PHE 0.010 0.001 PHE R 282 TYR 0.007 0.001 TYR R 308 ARG 0.004 0.001 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: R 72 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7812 (mp) outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.2141 time to fit residues: 6.1698 Evaluate side-chains 25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.0070 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.130372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116099 restraints weight = 3130.432| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.75 r_work: 0.3211 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2198 Z= 0.151 Angle : 0.442 5.084 3013 Z= 0.244 Chirality : 0.038 0.108 372 Planarity : 0.003 0.025 359 Dihedral : 4.045 16.709 310 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.85 % Allowed : 18.06 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.63 (0.52), residues: 277 helix: 2.54 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.81 (0.81), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 313 HIS 0.002 0.001 HIS R 93 PHE 0.009 0.001 PHE R 282 TYR 0.006 0.001 TYR R 308 ARG 0.006 0.001 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: R 72 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7776 (mp) REVERT: R 334 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8105 (mp) outliers start: 4 outliers final: 2 residues processed: 26 average time/residue: 0.2058 time to fit residues: 6.1384 Evaluate side-chains 26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 334 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 0.0270 chunk 10 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.129775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.115540 restraints weight = 3130.471| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.73 r_work: 0.3205 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2198 Z= 0.166 Angle : 0.445 5.127 3013 Z= 0.246 Chirality : 0.038 0.108 372 Planarity : 0.003 0.025 359 Dihedral : 4.058 16.587 310 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.31 % Allowed : 18.06 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.59 (0.51), residues: 277 helix: 2.51 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.84 (0.81), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.002 0.001 HIS R 93 PHE 0.010 0.001 PHE R 282 TYR 0.006 0.001 TYR R 308 ARG 0.005 0.001 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: R 72 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7796 (mp) REVERT: R 334 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8104 (mp) outliers start: 5 outliers final: 3 residues processed: 28 average time/residue: 0.1919 time to fit residues: 6.2831 Evaluate side-chains 26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 334 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.127811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.112930 restraints weight = 3153.857| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.90 r_work: 0.3168 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2198 Z= 0.196 Angle : 0.466 5.145 3013 Z= 0.257 Chirality : 0.039 0.111 372 Planarity : 0.003 0.026 359 Dihedral : 4.178 16.593 310 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.31 % Allowed : 18.52 % Favored : 79.17 % 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 (0.51), residues: 277 helix: 2.40 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.89 (0.81), residues: 55 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 0.011 0.001 PHE R 282 TYR 0.011 0.001 TYR R 185 ARG 0.004 0.001 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: R 72 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7826 (mp) REVERT: R 215 MET cc_start: 0.7841 (mtp) cc_final: 0.7523 (mtp) outliers start: 5 outliers final: 3 residues processed: 26 average time/residue: 0.2007 time to fit residues: 5.9890 Evaluate side-chains 25 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.111556 restraints weight = 3176.340| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.75 r_work: 0.3153 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2198 Z= 0.244 Angle : 0.507 5.202 3013 Z= 0.278 Chirality : 0.039 0.112 372 Planarity : 0.003 0.027 359 Dihedral : 4.271 16.606 310 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.85 % Allowed : 18.98 % Favored : 79.17 % 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: 2.22 (0.51), residues: 277 helix: 2.24 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.89 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.012 0.001 PHE R 282 TYR 0.009 0.001 TYR R 185 ARG 0.005 0.001 ARG R 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: R 72 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7814 (mp) REVERT: R 215 MET cc_start: 0.7842 (mtp) cc_final: 0.7512 (mtp) outliers start: 4 outliers final: 3 residues processed: 26 average time/residue: 0.1955 time to fit residues: 5.8932 Evaluate side-chains 26 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 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 = 0.3415 r_free = 0.3415 target = 0.126241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.112046 restraints weight = 3138.577| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.74 r_work: 0.3159 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2198 Z= 0.225 Angle : 0.500 5.149 3013 Z= 0.276 Chirality : 0.039 0.111 372 Planarity : 0.003 0.026 359 Dihedral : 4.239 16.839 310 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.85 % Allowed : 18.98 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.51), residues: 277 helix: 2.22 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -1.83 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.011 0.001 PHE R 282 TYR 0.019 0.002 TYR R 185 ARG 0.005 0.001 ARG R 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1543.84 seconds wall clock time: 27 minutes 59.64 seconds (1679.64 seconds total)