Starting phenix.real_space_refine on Wed Sep 17 03:00:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvh_61839/09_2025/9jvh_61839.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvh_61839/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jvh_61839/09_2025/9jvh_61839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvh_61839/09_2025/9jvh_61839.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jvh_61839/09_2025/9jvh_61839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvh_61839/09_2025/9jvh_61839.map" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 9, 'ASP:plan': 5, 'HIS:plan': 2, 'TRP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 6, 'ASN:plan1': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 158 Time building chain proxies: 1.30, per 1000 atoms: 0.60 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: 0.29 Conformation dependent library (CDL) restraints added in 64.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.08 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: 0.38 Time building geometry restraints manager: 0.35 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: 2.970 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.210 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.350 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG R 204 TYR 0.018 0.002 TYR R 242 PHE 0.027 0.003 PHE R 276 TRP 0.010 0.002 TRP R 75 HIS 0.006 0.002 HIS R 167 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 2240) covalent geometry : angle 0.81163 ( 3071) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.81764 ( 2) hydrogen bonds : bond 0.13771 ( 153) hydrogen bonds : angle 6.12589 ( 453) *********************** 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 : 0.046 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: 0.3660 time to fit residues: 16.6139 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 : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 13 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.0970 chunk 25 optimal weight: 0.0570 chunk 26 optimal weight: 0.6980 overall best weight: 0.1696 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.138783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.132052 restraints weight = 3658.516| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.69 r_work: 0.3802 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2241 Z= 0.135 Angle : 0.604 7.789 3073 Z= 0.317 Chirality : 0.044 0.205 364 Planarity : 0.004 0.027 381 Dihedral : 4.358 14.183 318 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.32 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.49), residues: 292 helix: 0.85 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -3.58 (0.56), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 187 TYR 0.009 0.002 TYR R 104 PHE 0.017 0.002 PHE R 276 TRP 0.014 0.002 TRP R 75 HIS 0.008 0.001 HIS R 87 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 2240) covalent geometry : angle 0.60361 ( 3071) SS BOND : bond 0.00181 ( 1) SS BOND : angle 0.74345 ( 2) hydrogen bonds : bond 0.04079 ( 153) hydrogen bonds : angle 4.34425 ( 453) *********************** 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 46 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.082 Fit side-chains REVERT: R 137 VAL cc_start: 0.7862 (m) cc_final: 0.7629 (p) REVERT: R 242 TYR cc_start: 0.8189 (t80) cc_final: 0.7582 (t80) outliers start: 8 outliers final: 0 residues processed: 40 average time/residue: 0.3862 time to fit residues: 15.9343 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 : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 17 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 19 optimal weight: 0.0980 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.137216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.130485 restraints weight = 3731.222| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.68 r_work: 0.3773 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2241 Z= 0.164 Angle : 0.601 7.522 3073 Z= 0.321 Chirality : 0.043 0.124 364 Planarity : 0.004 0.043 381 Dihedral : 4.240 16.069 318 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.43 % Allowed : 12.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.49), residues: 292 helix: 0.93 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -3.52 (0.57), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 208 TYR 0.010 0.002 TYR R 104 PHE 0.017 0.002 PHE R 276 TRP 0.014 0.001 TRP R 75 HIS 0.005 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 2240) covalent geometry : angle 0.60118 ( 3071) SS BOND : bond 0.00203 ( 1) SS BOND : angle 0.64399 ( 2) hydrogen bonds : bond 0.04244 ( 153) hydrogen bonds : angle 4.18555 ( 453) *********************** 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 43 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.082 Fit side-chains REVERT: R 242 TYR cc_start: 0.8172 (t80) cc_final: 0.7849 (t80) outliers start: 5 outliers final: 0 residues processed: 42 average time/residue: 0.4024 time to fit residues: 17.3893 Evaluate side-chains 36 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 19 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 3 optimal weight: 0.0870 chunk 24 optimal weight: 0.2980 overall best weight: 0.2958 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.137291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.130611 restraints weight = 3691.252| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.68 r_work: 0.3778 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2241 Z= 0.157 Angle : 0.593 7.806 3073 Z= 0.317 Chirality : 0.044 0.161 364 Planarity : 0.004 0.045 381 Dihedral : 4.174 17.329 318 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.37 % Allowed : 14.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.50), residues: 292 helix: 1.01 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -3.51 (0.59), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 208 TYR 0.010 0.002 TYR R 78 PHE 0.016 0.002 PHE R 276 TRP 0.015 0.001 TRP R 75 HIS 0.004 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 2240) covalent geometry : angle 0.59267 ( 3071) SS BOND : bond 0.00154 ( 1) SS BOND : angle 0.63040 ( 2) hydrogen bonds : bond 0.04165 ( 153) hydrogen bonds : angle 4.18168 ( 453) *********************** 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 47 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.076 Fit side-chains REVERT: R 137 VAL cc_start: 0.7890 (m) cc_final: 0.7631 (p) REVERT: R 171 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.6531 (t80) REVERT: R 183 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7833 (tpt) REVERT: R 242 TYR cc_start: 0.8138 (t80) cc_final: 0.7782 (t80) outliers start: 9 outliers final: 2 residues processed: 41 average time/residue: 0.4124 time to fit residues: 17.3844 Evaluate side-chains 39 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.081 ------------------------------------------------------------------------------- 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 180 VAL Chi-restraints excluded: chain R residue 183 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 21 optimal weight: 0.1980 chunk 11 optimal weight: 0.0040 chunk 25 optimal weight: 0.2980 chunk 8 optimal weight: 0.0970 chunk 14 optimal weight: 0.0070 chunk 23 optimal weight: 0.0870 chunk 19 optimal weight: 0.0980 overall best weight: 0.0586 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.142030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.135343 restraints weight = 3727.298| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 1.65 r_work: 0.3847 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 2241 Z= 0.110 Angle : 0.532 5.407 3073 Z= 0.282 Chirality : 0.040 0.130 364 Planarity : 0.003 0.035 381 Dihedral : 3.748 13.846 318 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.88 % Allowed : 15.53 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.50), residues: 292 helix: 1.38 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -3.21 (0.60), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 208 TYR 0.007 0.001 TYR R 68 PHE 0.012 0.001 PHE R 267 TRP 0.010 0.001 TRP R 75 HIS 0.002 0.000 HIS R 271 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 2240) covalent geometry : angle 0.53231 ( 3071) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.59836 ( 2) hydrogen bonds : bond 0.03247 ( 153) hydrogen bonds : angle 3.89907 ( 453) *********************** 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 44 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: R 137 VAL cc_start: 0.7829 (m) cc_final: 0.7598 (p) REVERT: R 171 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7626 (t80) outliers start: 8 outliers final: 1 residues processed: 39 average time/residue: 0.4192 time to fit residues: 16.7972 Evaluate side-chains 36 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 23 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.0980 chunk 18 optimal weight: 0.0040 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 21 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 overall best weight: 0.0770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.142749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.135991 restraints weight = 3637.781| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.66 r_work: 0.3854 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2241 Z= 0.105 Angle : 0.509 5.440 3073 Z= 0.271 Chirality : 0.040 0.119 364 Planarity : 0.004 0.047 381 Dihedral : 3.549 12.215 318 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.40 % Allowed : 17.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.50), residues: 292 helix: 1.62 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -3.29 (0.58), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 208 TYR 0.007 0.001 TYR R 104 PHE 0.011 0.001 PHE R 267 TRP 0.008 0.001 TRP R 75 HIS 0.002 0.001 HIS R 271 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 2240) covalent geometry : angle 0.50897 ( 3071) SS BOND : bond 0.00137 ( 1) SS BOND : angle 0.62937 ( 2) hydrogen bonds : bond 0.03166 ( 153) hydrogen bonds : angle 3.77536 ( 453) *********************** 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 44 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.083 Fit side-chains REVERT: R 42 TRP cc_start: 0.8005 (t-100) cc_final: 0.7790 (t-100) REVERT: R 137 VAL cc_start: 0.7848 (m) cc_final: 0.7629 (p) REVERT: R 171 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7474 (t80) outliers start: 7 outliers final: 2 residues processed: 40 average time/residue: 0.3429 time to fit residues: 14.1738 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 : 0.055 ------------------------------------------------------------------------------- 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 306 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 0.0970 chunk 23 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 16 optimal weight: 0.1980 overall best weight: 0.2978 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.138263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.131557 restraints weight = 3668.193| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.67 r_work: 0.3789 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2241 Z= 0.153 Angle : 0.556 5.485 3073 Z= 0.298 Chirality : 0.043 0.132 364 Planarity : 0.004 0.051 381 Dihedral : 3.800 16.096 318 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.43 % Allowed : 18.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.50), residues: 292 helix: 1.49 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -3.26 (0.63), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 208 TYR 0.023 0.002 TYR R 242 PHE 0.016 0.002 PHE R 99 TRP 0.010 0.001 TRP R 144 HIS 0.004 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 2240) covalent geometry : angle 0.55601 ( 3071) SS BOND : bond 0.00121 ( 1) SS BOND : angle 0.51659 ( 2) hydrogen bonds : bond 0.03815 ( 153) hydrogen bonds : angle 3.98814 ( 453) *********************** 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 : 0.059 Fit side-chains REVERT: R 42 TRP cc_start: 0.7997 (t-100) cc_final: 0.7791 (t-100) REVERT: R 132 ARG cc_start: 0.7574 (mtp85) cc_final: 0.7365 (mtp-110) REVERT: R 242 TYR cc_start: 0.8189 (t80) cc_final: 0.7842 (t80) outliers start: 5 outliers final: 1 residues processed: 42 average time/residue: 0.3741 time to fit residues: 16.1538 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 : 0.074 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.1980 chunk 12 optimal weight: 0.2980 chunk 25 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 0.0970 chunk 28 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.0970 chunk 3 optimal weight: 0.0670 chunk 19 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 overall best weight: 0.1514 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.140587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.133697 restraints weight = 3697.484| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 1.70 r_work: 0.3816 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2500 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 : 0.546 5.444 3073 Z= 0.290 Chirality : 0.042 0.139 364 Planarity : 0.004 0.044 381 Dihedral : 3.683 13.578 318 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.46 % Allowed : 21.36 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.51), residues: 292 helix: 1.59 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -3.19 (0.62), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 208 TYR 0.016 0.002 TYR R 242 PHE 0.013 0.001 PHE R 99 TRP 0.011 0.001 TRP R 75 HIS 0.003 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 2240) covalent geometry : angle 0.54568 ( 3071) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.43707 ( 2) hydrogen bonds : bond 0.03409 ( 153) hydrogen bonds : angle 3.92463 ( 453) *********************** 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: 3 poor density : 40 time to evaluate : 0.057 Fit side-chains REVERT: R 45 TYR cc_start: 0.6532 (t80) cc_final: 0.6111 (t80) REVERT: R 132 ARG cc_start: 0.7552 (mtp85) cc_final: 0.7350 (mtp-110) REVERT: R 137 VAL cc_start: 0.7886 (m) cc_final: 0.7610 (p) REVERT: R 242 TYR cc_start: 0.8129 (t80) cc_final: 0.7848 (t80) outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.3424 time to fit residues: 14.1728 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 : 0.081 ------------------------------------------------------------------------------- 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 14 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 3 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 17 optimal weight: 0.3980 chunk 12 optimal weight: 0.3980 chunk 22 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 overall best weight: 0.1778 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.140339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.133458 restraints weight = 3709.292| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.71 r_work: 0.3812 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2583 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= 0.126 Angle : 0.549 5.452 3073 Z= 0.292 Chirality : 0.042 0.137 364 Planarity : 0.004 0.057 381 Dihedral : 3.675 13.944 318 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.46 % Allowed : 20.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.51), residues: 292 helix: 1.65 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -3.28 (0.60), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 208 TYR 0.017 0.002 TYR R 242 PHE 0.014 0.002 PHE R 99 TRP 0.009 0.001 TRP R 75 HIS 0.003 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 2240) covalent geometry : angle 0.54952 ( 3071) SS BOND : bond 0.00155 ( 1) SS BOND : angle 0.45809 ( 2) hydrogen bonds : bond 0.03486 ( 153) hydrogen bonds : angle 3.92341 ( 453) *********************** 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 42 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.075 Fit side-chains REVERT: R 27 ILE cc_start: 0.7902 (pp) cc_final: 0.7511 (pp) REVERT: R 137 VAL cc_start: 0.7890 (m) cc_final: 0.7614 (p) outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.2571 time to fit residues: 10.6478 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 : 0.045 ------------------------------------------------------------------------------- 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 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.0670 chunk 25 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 18 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 overall best weight: 0.2296 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.139950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.132969 restraints weight = 3727.221| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.72 r_work: 0.3804 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2241 Z= 0.141 Angle : 0.571 5.439 3073 Z= 0.306 Chirality : 0.042 0.141 364 Planarity : 0.005 0.062 381 Dihedral : 3.887 16.249 318 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.49 % Allowed : 22.33 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.51), residues: 292 helix: 1.59 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -3.32 (0.61), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 208 TYR 0.012 0.002 TYR R 78 PHE 0.015 0.002 PHE R 99 TRP 0.011 0.001 TRP R 75 HIS 0.004 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 2240) covalent geometry : angle 0.57080 ( 3071) SS BOND : bond 0.00130 ( 1) SS BOND : angle 0.47358 ( 2) hydrogen bonds : bond 0.03645 ( 153) hydrogen bonds : angle 4.04631 ( 453) ********************** 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: 1 poor density : 38 time to evaluate : 0.057 Fit side-chains REVERT: R 132 ARG cc_start: 0.7591 (mtp85) cc_final: 0.7354 (mtp-110) REVERT: R 137 VAL cc_start: 0.7907 (m) cc_final: 0.7643 (p) outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.3613 time to fit residues: 14.1413 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 : 0.073 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.0670 chunk 3 optimal weight: 0.0370 chunk 5 optimal weight: 0.4980 chunk 23 optimal weight: 0.0770 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 overall best weight: 0.1754 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.140884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.133961 restraints weight = 3762.647| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.66 r_work: 0.3818 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2241 Z= 0.128 Angle : 0.558 5.472 3073 Z= 0.298 Chirality : 0.042 0.142 364 Planarity : 0.005 0.060 381 Dihedral : 3.772 15.005 318 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.46 % Allowed : 21.84 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.50), residues: 292 helix: 1.61 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -3.59 (0.54), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 208 TYR 0.011 0.002 TYR R 78 PHE 0.014 0.001 PHE R 99 TRP 0.009 0.001 TRP R 75 HIS 0.003 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 2240) covalent geometry : angle 0.55821 ( 3071) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.48530 ( 2) hydrogen bonds : bond 0.03461 ( 153) hydrogen bonds : angle 4.00766 ( 453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1021.08 seconds wall clock time: 18 minutes 22.50 seconds (1102.50 seconds total)