Starting phenix.real_space_refine on Wed Mar 5 15:10:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvh_61839/03_2025/9jvh_61839.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvh_61839/03_2025/9jvh_61839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jvh_61839/03_2025/9jvh_61839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvh_61839/03_2025/9jvh_61839.map" model { file = "/net/cci-nas-00/data/ceres_data/9jvh_61839/03_2025/9jvh_61839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvh_61839/03_2025/9jvh_61839.cif" } resolution = 2.76 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 1434 2.51 5 N 368 2.21 5 O 365 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: 2180 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2180 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 158 Time building chain proxies: 2.32, per 1000 atoms: 1.06 Number of scatterers: 2180 At special positions: 0 Unit cell: (63.6, 64.66, 69.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 13 16.00 O 365 8.00 N 368 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 92 " - pdb=" SG CYS R 170 " 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: 0.52 Conformation dependent library (CDL) restraints added in 272.4 milliseconds 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 79.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 20 through 50 removed outlier: 3.523A pdb=" N SER R 24 " --> pdb=" O LEU R 20 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE R 27 " --> pdb=" O PRO R 23 " (cutoff:3.500A) Proline residue: R 35 - end of helix Processing helix chain 'R' and resid 53 through 81 removed outlier: 3.757A pdb=" N TYR R 57 " --> pdb=" O GLU R 53 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA R 64 " --> pdb=" O ASN R 60 " (cutoff:3.500A) Proline residue: R 73 - end of helix Processing helix chain 'R' and resid 88 through 122 removed outlier: 3.852A pdb=" N CYS R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS R 93 " --> pdb=" O PRO R 89 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU R 94 " --> pdb=" O GLY R 90 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE R 97 " --> pdb=" O LYS R 93 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE R 103 " --> pdb=" O PHE R 99 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TYR R 104 " --> pdb=" O TYR R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 151 Processing helix chain 'R' and resid 152 through 157 removed outlier: 4.371A pdb=" N PHE R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS R 157 " --> pdb=" O ALA R 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 152 through 157' Processing helix chain 'R' and resid 177 through 190 removed outlier: 3.573A pdb=" N ALA R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP R 182 " --> pdb=" O ARG R 178 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR R 186 " --> pdb=" O TRP R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 209 Processing helix chain 'R' and resid 217 through 256 removed outlier: 3.583A pdb=" N LEU R 227 " --> pdb=" O LYS R 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE R 232 " --> pdb=" O ALA R 228 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL R 235 " --> pdb=" O LEU R 231 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU R 236 " --> pdb=" O ILE R 232 " (cutoff:3.500A) Proline residue: R 241 - end of helix removed outlier: 3.559A pdb=" N TYR R 253 " --> pdb=" O ARG R 249 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY R 255 " --> pdb=" O ALA R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 264 Processing helix chain 'R' and resid 265 through 276 removed outlier: 4.708A pdb=" N ALA R 269 " --> pdb=" O ARG R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 280 Processing helix chain 'R' and resid 282 through 290 removed outlier: 3.647A pdb=" N ILE R 286 " --> pdb=" O VAL R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 304 153 hydrogen bonds defined for protein. 453 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: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 674 1.34 - 1.46: 413 1.46 - 1.57: 1136 1.57 - 1.69: 0 1.69 - 1.81: 17 Bond restraints: 2240 Sorted by residual: bond pdb=" CA TRP R 85 " pdb=" CB TRP R 85 " ideal model delta sigma weight residual 1.527 1.494 0.033 1.75e-02 3.27e+03 3.53e+00 bond pdb=" CG LEU R 236 " pdb=" CD2 LEU R 236 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.12e+00 bond pdb=" CA ILE R 86 " pdb=" C ILE R 86 " ideal model delta sigma weight residual 1.530 1.518 0.012 1.12e-02 7.97e+03 1.09e+00 bond pdb=" CB TRP R 196 " pdb=" CG TRP R 196 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.09e+00 bond pdb=" CB PRO R 22 " pdb=" CG PRO R 22 " ideal model delta sigma weight residual 1.492 1.442 0.050 5.00e-02 4.00e+02 9.96e-01 ... (remaining 2235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 3037 2.94 - 5.87: 30 5.87 - 8.81: 3 8.81 - 11.74: 0 11.74 - 14.68: 1 Bond angle restraints: 3071 Sorted by residual: angle pdb=" C ILE R 86 " pdb=" CA ILE R 86 " pdb=" CB ILE R 86 " ideal model delta sigma weight residual 112.19 97.51 14.68 1.15e+00 7.56e-01 1.63e+02 angle pdb=" N PHE R 169 " pdb=" CA PHE R 169 " pdb=" C PHE R 169 " ideal model delta sigma weight residual 111.24 118.74 -7.50 1.38e+00 5.25e-01 2.95e+01 angle pdb=" N THR R 168 " pdb=" CA THR R 168 " pdb=" C THR R 168 " ideal model delta sigma weight residual 114.75 109.48 5.27 1.26e+00 6.30e-01 1.75e+01 angle pdb=" N TRP R 85 " pdb=" CA TRP R 85 " pdb=" C TRP R 85 " ideal model delta sigma weight residual 107.69 99.95 7.74 2.01e+00 2.48e-01 1.48e+01 angle pdb=" C PHE R 169 " pdb=" CA PHE R 169 " pdb=" CB PHE R 169 " ideal model delta sigma weight residual 112.09 107.33 4.76 1.54e+00 4.22e-01 9.56e+00 ... (remaining 3066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.02: 1143 14.02 - 28.05: 112 28.05 - 42.07: 32 42.07 - 56.09: 3 56.09 - 70.11: 3 Dihedral angle restraints: 1293 sinusoidal: 422 harmonic: 871 Sorted by residual: dihedral pdb=" CB CYS R 92 " pdb=" SG CYS R 92 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual -86.00 -138.41 52.41 1 1.00e+01 1.00e-02 3.74e+01 dihedral pdb=" C ILE R 86 " pdb=" N ILE R 86 " pdb=" CA ILE R 86 " pdb=" CB ILE R 86 " ideal model delta harmonic sigma weight residual -122.00 -107.01 -14.99 0 2.50e+00 1.60e-01 3.60e+01 dihedral pdb=" CA CYS R 281 " pdb=" C CYS R 281 " pdb=" N VAL R 282 " pdb=" CA VAL R 282 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 1290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 330 0.084 - 0.167: 32 0.167 - 0.250: 0 0.250 - 0.334: 1 0.334 - 0.417: 1 Chirality restraints: 364 Sorted by residual: chirality pdb=" CA ILE R 86 " pdb=" N ILE R 86 " pdb=" C ILE R 86 " pdb=" CB ILE R 86 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CA PHE R 169 " pdb=" N PHE R 169 " pdb=" C PHE R 169 " pdb=" CB PHE R 169 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA HIS R 87 " pdb=" N HIS R 87 " pdb=" C HIS R 87 " pdb=" CB HIS R 87 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 361 not shown) Planarity restraints: 381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 276 " -0.014 2.00e-02 2.50e+03 1.25e-02 2.72e+00 pdb=" CG PHE R 276 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE R 276 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 276 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE R 276 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 276 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE R 276 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS R 123 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO R 124 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO R 124 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 124 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 240 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO R 241 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO R 241 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 241 " 0.017 5.00e-02 4.00e+02 ... (remaining 378 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 820 2.88 - 3.38: 2304 3.38 - 3.89: 3629 3.89 - 4.39: 3931 4.39 - 4.90: 6673 Nonbonded interactions: 17357 Sorted by model distance: nonbonded pdb=" O SER R 278 " pdb=" OG SER R 278 " model vdw 2.375 3.040 nonbonded pdb=" OD1 ASN R 60 " pdb=" OG SER R 140 " model vdw 2.375 3.040 nonbonded pdb=" OH TYR R 78 " pdb=" OE1 GLU R 172 " model vdw 2.397 3.040 nonbonded pdb=" O GLY R 33 " pdb=" ND2 ASN R 37 " model vdw 2.416 3.120 nonbonded pdb=" N GLU R 53 " pdb=" OE1 GLU R 53 " model vdw 2.445 3.120 ... (remaining 17352 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: 1.200 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.860 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 2240 Z= 0.346 Angle : 0.812 14.676 3071 Z= 0.494 Chirality : 0.054 0.417 364 Planarity : 0.004 0.032 381 Dihedral : 12.931 70.113 726 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 8.33 % 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: -1.37 (0.49), residues: 292 helix: 0.34 (0.37), residues: 205 sheet: None (None), residues: 0 loop : -4.05 (0.52), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 75 HIS 0.006 0.002 HIS R 167 PHE 0.027 0.003 PHE R 276 TYR 0.018 0.002 TYR R 242 ARG 0.005 0.001 ARG R 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.218 Fit side-chains REVERT: R 100 TYR cc_start: 0.7995 (m-80) cc_final: 0.7775 (m-80) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.7335 time to fit residues: 33.4482 Evaluate side-chains 38 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 12 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.0000 chunk 11 optimal weight: 0.0270 chunk 22 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.1980 chunk 16 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 overall best weight: 0.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.139532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.132911 restraints weight = 3557.941| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.63 r_work: 0.3816 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2240 Z= 0.183 Angle : 0.597 7.674 3071 Z= 0.312 Chirality : 0.044 0.195 364 Planarity : 0.004 0.027 381 Dihedral : 4.302 12.982 318 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.88 % Allowed : 9.22 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.54 (0.49), residues: 292 helix: 0.84 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -3.61 (0.56), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 75 HIS 0.008 0.001 HIS R 87 PHE 0.016 0.002 PHE R 276 TYR 0.008 0.002 TYR R 104 ARG 0.003 0.000 ARG R 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.248 Fit side-chains REVERT: R 137 VAL cc_start: 0.7847 (m) cc_final: 0.7621 (p) REVERT: R 242 TYR cc_start: 0.8160 (t80) cc_final: 0.7547 (t80) outliers start: 8 outliers final: 0 residues processed: 41 average time/residue: 0.7282 time to fit residues: 30.9545 Evaluate side-chains 40 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 5 optimal weight: 0.2980 chunk 12 optimal weight: 0.3980 chunk 16 optimal weight: 0.0000 chunk 25 optimal weight: 0.2980 chunk 18 optimal weight: 0.2980 chunk 11 optimal weight: 0.4980 overall best weight: 0.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN R 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.138162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.131460 restraints weight = 3610.560| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.63 r_work: 0.3790 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2240 Z= 0.213 Angle : 0.580 7.159 3071 Z= 0.309 Chirality : 0.042 0.120 364 Planarity : 0.004 0.044 381 Dihedral : 4.104 14.467 318 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.94 % Allowed : 12.62 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.23 (0.50), residues: 292 helix: 1.04 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -3.38 (0.59), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 75 HIS 0.004 0.001 HIS R 243 PHE 0.015 0.002 PHE R 99 TYR 0.009 0.002 TYR R 78 ARG 0.007 0.001 ARG R 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.244 Fit side-chains REVERT: R 242 TYR cc_start: 0.8098 (t80) cc_final: 0.7839 (t80) outliers start: 4 outliers final: 0 residues processed: 42 average time/residue: 0.8079 time to fit residues: 35.0904 Evaluate side-chains 35 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 12 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 4 optimal weight: 0.0980 chunk 21 optimal weight: 0.3980 chunk 26 optimal weight: 0.1980 chunk 25 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 6 optimal weight: 0.0980 overall best weight: 0.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN R 60 ASN R 184 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.139178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.132543 restraints weight = 3612.347| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.65 r_work: 0.3805 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2240 Z= 0.191 Angle : 0.560 6.974 3071 Z= 0.298 Chirality : 0.042 0.145 364 Planarity : 0.004 0.041 381 Dihedral : 3.953 14.573 318 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.40 % Allowed : 15.05 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.50), residues: 292 helix: 1.17 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -3.33 (0.59), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 75 HIS 0.003 0.001 HIS R 243 PHE 0.014 0.002 PHE R 276 TYR 0.009 0.001 TYR R 78 ARG 0.008 0.001 ARG R 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.220 Fit side-chains REVERT: R 137 VAL cc_start: 0.7872 (m) cc_final: 0.7629 (p) outliers start: 7 outliers final: 3 residues processed: 38 average time/residue: 0.8393 time to fit residues: 32.9551 Evaluate side-chains 37 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 HIS Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 22 optimal weight: 0.1980 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 13 optimal weight: 0.4980 chunk 26 optimal weight: 0.0870 chunk 28 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 overall best weight: 0.1956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN R 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.139577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.132982 restraints weight = 3725.331| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.64 r_work: 0.3812 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2240 Z= 0.194 Angle : 0.563 7.296 3071 Z= 0.300 Chirality : 0.042 0.139 364 Planarity : 0.004 0.044 381 Dihedral : 3.982 14.466 318 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.88 % Allowed : 16.02 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.04 (0.50), residues: 292 helix: 1.24 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -3.34 (0.59), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 75 HIS 0.004 0.001 HIS R 243 PHE 0.018 0.002 PHE R 276 TYR 0.022 0.002 TYR R 242 ARG 0.010 0.001 ARG R 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.234 Fit side-chains REVERT: R 137 VAL cc_start: 0.7880 (m) cc_final: 0.7655 (p) REVERT: R 171 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.6908 (t80) outliers start: 8 outliers final: 2 residues processed: 37 average time/residue: 0.7825 time to fit residues: 30.0335 Evaluate side-chains 38 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 HIS Chi-restraints excluded: chain R residue 171 PHE Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 0.1980 chunk 3 optimal weight: 0.0970 chunk 17 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 2 optimal weight: 0.0970 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 11 optimal weight: 0.0670 chunk 1 optimal weight: 0.6980 overall best weight: 0.1314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN R 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.140868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.134179 restraints weight = 3673.375| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.68 r_work: 0.3827 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2240 Z= 0.167 Angle : 0.525 5.426 3071 Z= 0.281 Chirality : 0.041 0.130 364 Planarity : 0.004 0.049 381 Dihedral : 3.777 13.241 318 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.88 % Allowed : 16.99 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.35 (0.51), residues: 292 helix: 1.42 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -3.12 (0.62), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 75 HIS 0.002 0.001 HIS R 271 PHE 0.012 0.001 PHE R 99 TYR 0.010 0.001 TYR R 242 ARG 0.010 0.001 ARG R 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.256 Fit side-chains REVERT: R 137 VAL cc_start: 0.7857 (m) cc_final: 0.7640 (p) outliers start: 8 outliers final: 2 residues processed: 39 average time/residue: 0.7355 time to fit residues: 29.7916 Evaluate side-chains 37 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 HIS Chi-restraints excluded: chain R residue 231 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 0.0270 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 chunk 21 optimal weight: 0.2980 chunk 27 optimal weight: 0.3980 chunk 24 optimal weight: 0.0870 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 0.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN R 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.140165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.133468 restraints weight = 3723.684| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.69 r_work: 0.3815 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2240 Z= 0.192 Angle : 0.544 5.452 3071 Z= 0.291 Chirality : 0.041 0.136 364 Planarity : 0.004 0.051 381 Dihedral : 3.772 14.239 318 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.94 % Allowed : 19.90 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.40 (0.51), residues: 292 helix: 1.49 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -3.22 (0.63), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 75 HIS 0.003 0.001 HIS R 243 PHE 0.014 0.002 PHE R 99 TYR 0.013 0.002 TYR R 242 ARG 0.012 0.001 ARG R 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.245 Fit side-chains REVERT: R 42 TRP cc_start: 0.7849 (t-100) cc_final: 0.7523 (t-100) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.7788 time to fit residues: 29.9351 Evaluate side-chains 39 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 HIS Chi-restraints excluded: chain R residue 231 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 15 optimal weight: 0.0870 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.0470 chunk 3 optimal weight: 0.0870 chunk 6 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 11 optimal weight: 0.0870 chunk 10 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 overall best weight: 0.0812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN R 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.143391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.136558 restraints weight = 3795.486| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.63 r_work: 0.3857 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2240 Z= 0.158 Angle : 0.522 5.480 3071 Z= 0.276 Chirality : 0.040 0.119 364 Planarity : 0.004 0.051 381 Dihedral : 3.554 12.568 318 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.43 % Allowed : 19.90 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.61 (0.50), residues: 292 helix: 1.69 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -3.41 (0.58), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 75 HIS 0.003 0.001 HIS R 243 PHE 0.012 0.001 PHE R 267 TYR 0.014 0.001 TYR R 242 ARG 0.012 0.001 ARG R 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.237 Fit side-chains REVERT: R 42 TRP cc_start: 0.7837 (t-100) cc_final: 0.7503 (t-100) REVERT: R 137 VAL cc_start: 0.7836 (m) cc_final: 0.7578 (p) outliers start: 5 outliers final: 1 residues processed: 39 average time/residue: 0.7220 time to fit residues: 29.2579 Evaluate side-chains 36 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 3 optimal weight: 0.0370 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 25 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 20 optimal weight: 0.0980 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.1658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN R 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.141324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.134509 restraints weight = 3716.713| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.68 r_work: 0.3829 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2240 Z= 0.185 Angle : 0.564 7.214 3071 Z= 0.294 Chirality : 0.042 0.144 364 Planarity : 0.004 0.053 381 Dihedral : 3.607 13.003 318 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.43 % Allowed : 19.90 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.53 (0.50), residues: 292 helix: 1.60 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -3.34 (0.59), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 75 HIS 0.003 0.001 HIS R 243 PHE 0.014 0.002 PHE R 109 TYR 0.013 0.001 TYR R 242 ARG 0.012 0.001 ARG R 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.243 Fit side-chains REVERT: R 42 TRP cc_start: 0.7854 (t-100) cc_final: 0.7535 (t-100) REVERT: R 137 VAL cc_start: 0.7882 (m) cc_final: 0.7632 (p) outliers start: 5 outliers final: 1 residues processed: 43 average time/residue: 0.6698 time to fit residues: 29.9816 Evaluate side-chains 40 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 25 optimal weight: 0.4980 chunk 18 optimal weight: 0.4980 chunk 20 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 0 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN R 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.137212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.130651 restraints weight = 3711.111| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.60 r_work: 0.3775 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 2240 Z= 0.295 Angle : 0.666 8.568 3071 Z= 0.344 Chirality : 0.049 0.304 364 Planarity : 0.005 0.059 381 Dihedral : 4.143 18.642 318 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.97 % Allowed : 22.82 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.00 (0.50), residues: 292 helix: 1.17 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -3.28 (0.62), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 75 HIS 0.006 0.002 HIS R 243 PHE 0.018 0.002 PHE R 276 TYR 0.016 0.002 TYR R 78 ARG 0.012 0.001 ARG R 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.264 Fit side-chains REVERT: R 171 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.6805 (t80) outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.8368 time to fit residues: 34.6695 Evaluate side-chains 41 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 HIS Chi-restraints excluded: chain R residue 171 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 0.0980 chunk 24 optimal weight: 0.0030 chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 chunk 3 optimal weight: 0.0670 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.1928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.139913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.133141 restraints weight = 3670.613| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.65 r_work: 0.3807 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2240 Z= 0.201 Angle : 0.627 8.339 3071 Z= 0.321 Chirality : 0.046 0.282 364 Planarity : 0.004 0.057 381 Dihedral : 3.974 15.012 318 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.46 % Allowed : 22.82 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.07 (0.50), residues: 292 helix: 1.23 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -3.29 (0.61), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 75 HIS 0.003 0.001 HIS R 243 PHE 0.014 0.002 PHE R 99 TYR 0.010 0.002 TYR R 78 ARG 0.013 0.001 ARG R 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1987.74 seconds wall clock time: 35 minutes 5.19 seconds (2105.19 seconds total)