Starting phenix.real_space_refine on Fri May 9 13:41:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvh_61839/05_2025/9jvh_61839.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvh_61839/05_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_61839/05_2025/9jvh_61839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvh_61839/05_2025/9jvh_61839.map" model { file = "/net/cci-nas-00/data/ceres_data/9jvh_61839/05_2025/9jvh_61839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvh_61839/05_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-5687/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: 2.31, 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: 0.57 Conformation dependent library (CDL) restraints added in 287.7 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: 0.52 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 1.210 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: 0.020 Process input model: 10.930 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- 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 2241 Z= 0.229 Angle : 0.812 14.676 3073 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 Details of bonding type rmsd hydrogen bonds : bond 0.13771 ( 153) hydrogen bonds : angle 6.12589 ( 453) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.81764 ( 2) covalent geometry : bond 0.00541 ( 2240) covalent geometry : angle 0.81163 ( 3071) *********************** 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 : 0.231 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: 0.7188 time to fit residues: 32.7652 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 : 0.231 ------------------------------------------------------------------------------- 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: 3.78 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 2241 Z= 0.129 Angle : 0.597 7.674 3073 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 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 153) hydrogen bonds : angle 4.32116 ( 453) SS BOND : bond 0.00191 ( 1) SS BOND : angle 0.72569 ( 2) covalent geometry : bond 0.00278 ( 2240) covalent geometry : angle 0.59709 ( 3071) *********************** 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 : 0.214 Fit side-chains REVERT: R 137 VAL cc_start: 0.7847 (m) cc_final: 0.7621 (p) REVERT: R 242 TYR cc_start: 0.8162 (t80) cc_final: 0.7547 (t80) outliers start: 8 outliers final: 0 residues processed: 41 average time/residue: 0.7392 time to fit residues: 31.4113 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 : 0.211 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.131465 restraints weight = 3610.560| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.63 r_work: 0.3791 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 2241 Z= 0.143 Angle : 0.580 7.159 3073 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 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 153) hydrogen bonds : angle 4.08959 ( 453) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.57322 ( 2) covalent geometry : bond 0.00333 ( 2240) covalent geometry : angle 0.57990 ( 3071) *********************** 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 : 0.241 Fit side-chains REVERT: R 242 TYR cc_start: 0.8096 (t80) cc_final: 0.7838 (t80) outliers start: 4 outliers final: 0 residues processed: 42 average time/residue: 0.7996 time to fit residues: 34.7177 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 : 0.231 ------------------------------------------------------------------------------- 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: 0.0980 chunk 26 optimal weight: 0.1980 chunk 25 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 6 optimal weight: 0.1980 overall best weight: 0.1580 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.140155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.133486 restraints weight = 3600.187| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 1.64 r_work: 0.3819 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2241 Z= 0.121 Angle : 0.547 6.557 3073 Z= 0.291 Chirality : 0.042 0.139 364 Planarity : 0.004 0.040 381 Dihedral : 3.872 13.369 318 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % 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: 0.07 (0.50), residues: 292 helix: 1.21 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -3.22 (0.60), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 75 HIS 0.002 0.001 HIS R 271 PHE 0.012 0.002 PHE R 99 TYR 0.008 0.001 TYR R 78 ARG 0.008 0.001 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 153) hydrogen bonds : angle 4.00066 ( 453) SS BOND : bond 0.00123 ( 1) SS BOND : angle 0.61677 ( 2) covalent geometry : bond 0.00275 ( 2240) covalent geometry : angle 0.54737 ( 3071) *********************** 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 : 0.212 Fit side-chains REVERT: R 137 VAL cc_start: 0.7860 (m) cc_final: 0.7617 (p) outliers start: 7 outliers final: 3 residues processed: 38 average time/residue: 0.8157 time to fit residues: 32.0201 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 : 0.208 ------------------------------------------------------------------------------- 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: 0.0870 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 26 optimal weight: 0.0870 chunk 28 optimal weight: 0.2980 chunk 17 optimal weight: 0.2980 overall best weight: 0.2136 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.139389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.132753 restraints weight = 3709.381| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.63 r_work: 0.3808 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2241 Z= 0.135 Angle : 0.567 7.211 3073 Z= 0.302 Chirality : 0.042 0.140 364 Planarity : 0.004 0.045 381 Dihedral : 3.954 14.369 318 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.40 % Allowed : 15.53 % Favored : 81.07 % 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: 1.24 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -3.27 (0.60), 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 0.023 0.002 TYR R 242 ARG 0.010 0.001 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 153) hydrogen bonds : angle 4.03704 ( 453) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.42636 ( 2) covalent geometry : bond 0.00311 ( 2240) covalent geometry : angle 0.56745 ( 3071) *********************** 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: 7 poor density : 36 time to evaluate : 0.242 Fit side-chains REVERT: R 137 VAL cc_start: 0.7876 (m) cc_final: 0.7655 (p) REVERT: R 171 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.6902 (t80) outliers start: 7 outliers final: 3 residues processed: 38 average time/residue: 0.8391 time to fit residues: 32.9877 Evaluate side-chains 38 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 231 LEU 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: 0.1980 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.0770 chunk 17 optimal weight: 0.3980 chunk 16 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 2 optimal weight: 0.0870 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 overall best weight: 0.1316 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.141241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.134582 restraints weight = 3651.487| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.63 r_work: 0.3837 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2241 Z= 0.115 Angle : 0.523 5.413 3073 Z= 0.280 Chirality : 0.041 0.131 364 Planarity : 0.004 0.050 381 Dihedral : 3.743 12.933 318 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.88 % Allowed : 17.48 % Favored : 78.64 % 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: 212 sheet: None (None), residues: 0 loop : -3.17 (0.64), residues: 80 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 0.002 PHE R 99 TYR 0.012 0.001 TYR R 242 ARG 0.011 0.001 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 153) hydrogen bonds : angle 3.91214 ( 453) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.55845 ( 2) covalent geometry : bond 0.00260 ( 2240) covalent geometry : angle 0.52295 ( 3071) *********************** 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 45 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.237 Fit side-chains REVERT: R 137 VAL cc_start: 0.7839 (m) cc_final: 0.7631 (p) outliers start: 8 outliers final: 1 residues processed: 38 average time/residue: 0.7363 time to fit residues: 29.0525 Evaluate side-chains 38 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.0070 chunk 16 optimal weight: 0.0050 chunk 6 optimal weight: 0.1980 chunk 21 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 0.0970 chunk 9 optimal weight: 0.1980 overall best weight: 0.0606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.143862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.137122 restraints weight = 3725.473| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.62 r_work: 0.3870 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 2241 Z= 0.106 Angle : 0.509 5.430 3073 Z= 0.271 Chirality : 0.040 0.118 364 Planarity : 0.004 0.046 381 Dihedral : 3.471 12.760 318 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.43 % Allowed : 19.42 % 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: 0.61 (0.51), residues: 292 helix: 1.65 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -3.35 (0.59), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 75 HIS 0.002 0.001 HIS R 271 PHE 0.012 0.002 PHE R 267 TYR 0.006 0.001 TYR R 242 ARG 0.012 0.001 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 153) hydrogen bonds : angle 3.76095 ( 453) SS BOND : bond 0.00156 ( 1) SS BOND : angle 0.64982 ( 2) covalent geometry : bond 0.00231 ( 2240) covalent geometry : angle 0.50890 ( 3071) *********************** 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 44 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.235 Fit side-chains REVERT: R 27 ILE cc_start: 0.7661 (pp) cc_final: 0.7448 (pp) REVERT: R 137 VAL cc_start: 0.7840 (m) cc_final: 0.7639 (p) outliers start: 5 outliers final: 1 residues processed: 40 average time/residue: 0.7023 time to fit residues: 29.2149 Evaluate side-chains 38 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 15 optimal weight: 0.0570 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.0570 chunk 3 optimal weight: 0.0970 chunk 6 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 10 optimal weight: 0.2980 chunk 27 optimal weight: 0.0670 overall best weight: 0.0752 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.143883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.136873 restraints weight = 3834.009| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.69 r_work: 0.3864 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2241 Z= 0.107 Angle : 0.513 5.449 3073 Z= 0.270 Chirality : 0.040 0.123 364 Planarity : 0.004 0.055 381 Dihedral : 3.422 11.854 318 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.40 % Allowed : 18.45 % 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: 0.73 (0.50), residues: 292 helix: 1.70 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -3.25 (0.59), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 42 HIS 0.003 0.001 HIS R 271 PHE 0.012 0.001 PHE R 267 TYR 0.007 0.001 TYR R 78 ARG 0.013 0.001 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 153) hydrogen bonds : angle 3.78787 ( 453) SS BOND : bond 0.00130 ( 1) SS BOND : angle 0.60186 ( 2) covalent geometry : bond 0.00241 ( 2240) covalent geometry : angle 0.51314 ( 3071) *********************** 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 48 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.217 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 43 average time/residue: 0.6365 time to fit residues: 28.4678 Evaluate side-chains 39 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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: 0.0970 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.0370 chunk 25 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 20 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 chunk 22 optimal weight: 0.3980 overall best weight: 0.2056 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.141112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.134162 restraints weight = 3723.459| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.72 r_work: 0.3825 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2241 Z= 0.134 Angle : 0.597 9.156 3073 Z= 0.309 Chirality : 0.044 0.149 364 Planarity : 0.004 0.059 381 Dihedral : 3.679 13.084 318 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % 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: 0.41 (0.50), residues: 292 helix: 1.50 (0.35), residues: 213 sheet: None (None), residues: 0 loop : -3.35 (0.59), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 42 HIS 0.003 0.001 HIS R 243 PHE 0.015 0.002 PHE R 99 TYR 0.012 0.002 TYR R 78 ARG 0.013 0.001 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 153) hydrogen bonds : angle 4.07179 ( 453) SS BOND : bond 0.00131 ( 1) SS BOND : angle 0.45213 ( 2) covalent geometry : bond 0.00312 ( 2240) covalent geometry : angle 0.59707 ( 3071) *********************** 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 44 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.227 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 42 average time/residue: 0.7069 time to fit residues: 30.8416 Evaluate side-chains 37 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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: 0.7980 chunk 12 optimal weight: 0.0980 chunk 6 optimal weight: 0.3980 chunk 14 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 20 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 0 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.138578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.131892 restraints weight = 3693.002| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.64 r_work: 0.3793 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2241 Z= 0.182 Angle : 0.698 12.218 3073 Z= 0.352 Chirality : 0.053 0.389 364 Planarity : 0.005 0.064 381 Dihedral : 4.187 17.833 318 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.97 % Allowed : 24.27 % Favored : 74.76 % 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 (0.49), residues: 292 helix: 1.14 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -3.39 (0.60), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 144 HIS 0.005 0.002 HIS R 87 PHE 0.017 0.002 PHE R 276 TYR 0.018 0.002 TYR R 242 ARG 0.014 0.001 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 153) hydrogen bonds : angle 4.37750 ( 453) SS BOND : bond 0.00143 ( 1) SS BOND : angle 0.73477 ( 2) covalent geometry : bond 0.00430 ( 2240) covalent geometry : angle 0.69768 ( 3071) ********************** 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 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 Fit side-chains REVERT: R 137 VAL cc_start: 0.7917 (m) cc_final: 0.7651 (p) outliers start: 2 outliers final: 1 residues processed: 38 average time/residue: 0.8401 time to fit residues: 32.9802 Evaluate side-chains 38 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.4980 chunk 1 optimal weight: 0.2980 chunk 12 optimal weight: 0.0980 chunk 24 optimal weight: 0.4980 chunk 8 optimal weight: 0.0980 chunk 0 optimal weight: 0.5980 chunk 13 optimal weight: 0.0050 chunk 27 optimal weight: 0.0970 chunk 3 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.1192 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.142508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.135537 restraints weight = 3666.547| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.63 r_work: 0.3842 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2241 Z= 0.126 Angle : 0.657 13.146 3073 Z= 0.322 Chirality : 0.049 0.386 364 Planarity : 0.004 0.061 381 Dihedral : 3.860 13.318 318 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.49 % Allowed : 24.76 % Favored : 74.76 % 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: 0.17 (0.49), residues: 292 helix: 1.28 (0.35), residues: 212 sheet: None (None), residues: 0 loop : -3.24 (0.61), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 42 HIS 0.003 0.001 HIS R 271 PHE 0.013 0.002 PHE R 99 TYR 0.010 0.001 TYR R 78 ARG 0.014 0.001 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 153) hydrogen bonds : angle 4.22015 ( 453) SS BOND : bond 0.00132 ( 1) SS BOND : angle 0.46699 ( 2) covalent geometry : bond 0.00283 ( 2240) covalent geometry : angle 0.65726 ( 3071) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2013.38 seconds wall clock time: 35 minutes 37.41 seconds (2137.41 seconds total)