Starting phenix.real_space_refine on Fri Aug 22 12:39:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggp_40016/08_2025/8ggp_40016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggp_40016/08_2025/8ggp_40016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggp_40016/08_2025/8ggp_40016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggp_40016/08_2025/8ggp_40016.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggp_40016/08_2025/8ggp_40016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggp_40016/08_2025/8ggp_40016.cif" } resolution = 3.2 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= 0.027 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 1394 2.51 5 N 328 2.21 5 O 340 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2075 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2060 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 7, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 10, 'TRP:plan': 1, 'ASP:plan': 6, 'GLN:plan1': 5, 'ARG:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 115 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.95, per 1000 atoms: 0.46 Number of scatterers: 2075 At special positions: 0 Unit cell: (57.2682, 80.6961, 62.4744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 13 16.00 O 340 8.00 N 328 7.00 C 1394 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.20 Conformation dependent library (CDL) restraints added in 88.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 90.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.578A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 removed outlier: 3.781A pdb=" N GLN R 65 " --> pdb=" O GLU R 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 62 through 65' Processing helix chain 'R' and resid 66 through 85 removed outlier: 4.135A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 97 removed outlier: 4.202A pdb=" N PHE R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.501A pdb=" N SER R 120 " --> pdb=" O CYS R 116 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.778A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 removed outlier: 3.520A pdb=" N ILE R 182 " --> pdb=" O HIS R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.718A pdb=" N VAL R 206 " --> pdb=" O ALA R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 271 through 299 removed outlier: 4.093A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.508A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.821A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 340 166 hydrogen bonds defined for protein. 498 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: 0.27 Time building geometry restraints manager: 0.26 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: 615 1.34 - 1.46: 495 1.46 - 1.58: 1004 1.58 - 1.70: 0 1.70 - 1.82: 17 Bond restraints: 2131 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.442 -0.048 2.00e-02 2.50e+03 5.73e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.569 -0.046 2.00e-02 2.50e+03 5.25e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.562 -0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " ideal model delta sigma weight residual 1.506 1.537 -0.031 2.00e-02 2.50e+03 2.44e+00 ... (remaining 2126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 2813 1.08 - 2.16: 100 2.16 - 3.25: 8 3.25 - 4.33: 7 4.33 - 5.41: 5 Bond angle restraints: 2933 Sorted by residual: angle pdb=" C SER R 207 " pdb=" N PHE R 208 " pdb=" CA PHE R 208 " ideal model delta sigma weight residual 122.46 119.21 3.25 1.80e+00 3.09e-01 3.26e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.04 -5.41 3.00e+00 1.11e-01 3.25e+00 angle pdb=" N VAL R 87 " pdb=" CA VAL R 87 " pdb=" C VAL R 87 " ideal model delta sigma weight residual 108.88 112.53 -3.65 2.16e+00 2.14e-01 2.86e+00 angle pdb=" C THR R 96 " pdb=" N LYS R 97 " pdb=" CA LYS R 97 " ideal model delta sigma weight residual 124.31 127.13 -2.82 1.67e+00 3.59e-01 2.85e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 115.86 -4.97 3.00e+00 1.11e-01 2.75e+00 ... (remaining 2928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.65: 1053 12.65 - 25.30: 111 25.30 - 37.95: 28 37.95 - 50.60: 12 50.60 - 63.25: 1 Dihedral angle restraints: 1205 sinusoidal: 378 harmonic: 827 Sorted by residual: dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA VAL R 295 " pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta harmonic sigma weight residual 180.00 -164.96 -15.04 0 5.00e+00 4.00e-02 9.04e+00 dihedral pdb=" CA ARG R 151 " pdb=" CB ARG R 151 " pdb=" CG ARG R 151 " pdb=" CD ARG R 151 " ideal model delta sinusoidal sigma weight residual -180.00 -130.02 -49.98 3 1.50e+01 4.44e-03 8.84e+00 ... (remaining 1202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 226 0.030 - 0.059: 101 0.059 - 0.089: 25 0.089 - 0.119: 14 0.119 - 0.149: 1 Chirality restraints: 367 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA TRP R 313 " pdb=" N TRP R 313 " pdb=" C TRP R 313 " pdb=" CB TRP R 313 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA PRO R 138 " pdb=" N PRO R 138 " pdb=" C PRO R 138 " pdb=" CB PRO R 138 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.05e-01 ... (remaining 364 not shown) Planarity restraints: 351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 313 " -0.007 2.00e-02 2.50e+03 9.51e-03 2.26e+00 pdb=" CG TRP R 313 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP R 313 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP R 313 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 313 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP R 313 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 313 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 313 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 313 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 313 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " 0.016 5.00e-02 4.00e+02 2.37e-02 8.98e-01 pdb=" N PRO R 323 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.014 5.00e-02 4.00e+02 2.10e-02 7.03e-01 pdb=" N PRO R 211 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.012 5.00e-02 4.00e+02 ... (remaining 348 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 590 2.82 - 3.34: 2039 3.34 - 3.86: 3309 3.86 - 4.38: 3397 4.38 - 4.90: 6312 Nonbonded interactions: 15647 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.298 3.040 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.305 3.120 nonbonded pdb=" O SER R 137 " pdb=" OG SER R 137 " model vdw 2.344 3.040 nonbonded pdb=" O THR R 189 " pdb=" OG1 THR R 189 " model vdw 2.491 3.040 nonbonded pdb=" OD1 ASN R 196 " pdb=" N GLN R 197 " model vdw 2.513 3.120 ... (remaining 15642 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 4.750 Find NCS groups from input model: 0.000 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2132 Z= 0.189 Angle : 0.522 5.412 2935 Z= 0.285 Chirality : 0.039 0.149 367 Planarity : 0.003 0.024 351 Dihedral : 12.492 63.247 664 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.89 (0.51), residues: 276 helix: 1.93 (0.35), residues: 220 sheet: None (None), residues: 0 loop : -1.52 (0.69), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.010 0.001 TYR R 174 PHE 0.010 0.001 PHE R 217 TRP 0.025 0.002 TRP R 313 HIS 0.003 0.001 HIS R 93 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 2131) covalent geometry : angle 0.52046 ( 2933) SS BOND : bond 0.00127 ( 1) SS BOND : angle 1.45246 ( 2) hydrogen bonds : bond 0.16196 ( 166) hydrogen bonds : angle 5.18511 ( 498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.079 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0569 time to fit residues: 1.3660 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.134564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117921 restraints weight = 2898.440| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.83 r_work: 0.3298 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2132 Z= 0.133 Angle : 0.469 5.426 2935 Z= 0.263 Chirality : 0.038 0.129 367 Planarity : 0.003 0.022 351 Dihedral : 4.246 17.963 309 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.03 % Allowed : 4.64 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.32 (0.51), residues: 276 helix: 2.19 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.63 (0.76), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 63 TYR 0.007 0.001 TYR R 308 PHE 0.009 0.001 PHE R 217 TRP 0.007 0.001 TRP R 313 HIS 0.002 0.001 HIS R 93 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 2131) covalent geometry : angle 0.46841 ( 2933) SS BOND : bond 0.00115 ( 1) SS BOND : angle 1.24106 ( 2) hydrogen bonds : bond 0.05884 ( 166) hydrogen bonds : angle 3.86688 ( 498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.077 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.0535 time to fit residues: 1.3026 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.0370 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.131659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115360 restraints weight = 2913.126| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.77 r_work: 0.3310 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2132 Z= 0.142 Angle : 0.466 5.463 2935 Z= 0.261 Chirality : 0.038 0.125 367 Planarity : 0.003 0.023 351 Dihedral : 4.275 17.897 309 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.03 % Allowed : 10.31 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.44 (0.51), residues: 276 helix: 2.30 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.72 (0.76), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.007 0.001 TYR R 199 PHE 0.009 0.001 PHE R 217 TRP 0.006 0.001 TRP R 313 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 2131) covalent geometry : angle 0.46550 ( 2933) SS BOND : bond 0.00106 ( 1) SS BOND : angle 1.23563 ( 2) hydrogen bonds : bond 0.06085 ( 166) hydrogen bonds : angle 3.75497 ( 498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.077 Fit side-chains REVERT: R 40 MET cc_start: 0.7204 (mtt) cc_final: 0.6942 (mtt) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.0907 time to fit residues: 1.8108 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124934 restraints weight = 2839.403| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.67 r_work: 0.3321 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2132 Z= 0.139 Angle : 0.458 5.465 2935 Z= 0.257 Chirality : 0.038 0.126 367 Planarity : 0.003 0.025 351 Dihedral : 4.233 17.913 309 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.03 % Allowed : 13.40 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.48 (0.51), residues: 276 helix: 2.34 (0.34), residues: 226 sheet: None (None), residues: 0 loop : -1.79 (0.77), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.006 0.001 TYR R 199 PHE 0.008 0.001 PHE R 217 TRP 0.005 0.001 TRP R 313 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 2131) covalent geometry : angle 0.45760 ( 2933) SS BOND : bond 0.00187 ( 1) SS BOND : angle 1.16686 ( 2) hydrogen bonds : bond 0.05970 ( 166) hydrogen bonds : angle 3.68364 ( 498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.078 Fit side-chains REVERT: R 40 MET cc_start: 0.7164 (mtt) cc_final: 0.6920 (mtt) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.0868 time to fit residues: 1.7408 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.132683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.116219 restraints weight = 2909.255| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.83 r_work: 0.3273 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2132 Z= 0.131 Angle : 0.448 5.480 2935 Z= 0.250 Chirality : 0.038 0.124 367 Planarity : 0.003 0.026 351 Dihedral : 4.185 17.959 309 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.03 % Allowed : 13.92 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.57 (0.51), residues: 276 helix: 2.41 (0.34), residues: 226 sheet: None (None), residues: 0 loop : -1.79 (0.76), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.006 0.001 TYR R 308 PHE 0.008 0.001 PHE R 217 TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 2131) covalent geometry : angle 0.44747 ( 2933) SS BOND : bond 0.00157 ( 1) SS BOND : angle 1.08008 ( 2) hydrogen bonds : bond 0.05716 ( 166) hydrogen bonds : angle 3.63088 ( 498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.078 Fit side-chains REVERT: R 40 MET cc_start: 0.7219 (mtt) cc_final: 0.6961 (mtt) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.0928 time to fit residues: 1.8516 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.129036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.112542 restraints weight = 2928.390| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.85 r_work: 0.3219 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2132 Z= 0.167 Angle : 0.485 5.531 2935 Z= 0.273 Chirality : 0.039 0.127 367 Planarity : 0.003 0.027 351 Dihedral : 4.345 17.789 309 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.55 % Allowed : 14.43 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.36 (0.51), residues: 276 helix: 2.27 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.95 (0.75), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.007 0.001 TYR R 199 PHE 0.010 0.001 PHE R 282 TRP 0.005 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 2131) covalent geometry : angle 0.48425 ( 2933) SS BOND : bond 0.00188 ( 1) SS BOND : angle 1.13968 ( 2) hydrogen bonds : bond 0.06724 ( 166) hydrogen bonds : angle 3.78043 ( 498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.088 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 17 average time/residue: 0.0546 time to fit residues: 1.2290 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.129383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.112987 restraints weight = 2935.090| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.82 r_work: 0.3219 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2132 Z= 0.161 Angle : 0.478 5.536 2935 Z= 0.269 Chirality : 0.039 0.127 367 Planarity : 0.003 0.028 351 Dihedral : 4.336 18.183 309 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 14.95 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.36 (0.51), residues: 276 helix: 2.29 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -2.00 (0.75), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 63 TYR 0.006 0.001 TYR R 199 PHE 0.009 0.001 PHE R 282 TRP 0.005 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 2131) covalent geometry : angle 0.47727 ( 2933) SS BOND : bond 0.00223 ( 1) SS BOND : angle 1.14174 ( 2) hydrogen bonds : bond 0.06573 ( 166) hydrogen bonds : angle 3.77133 ( 498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.079 Fit side-chains REVERT: R 40 MET cc_start: 0.7279 (mtt) cc_final: 0.7009 (mtt) outliers start: 4 outliers final: 3 residues processed: 18 average time/residue: 0.0509 time to fit residues: 1.1963 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.135251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119129 restraints weight = 2820.861| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.82 r_work: 0.3242 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2132 Z= 0.139 Angle : 0.453 5.482 2935 Z= 0.255 Chirality : 0.038 0.125 367 Planarity : 0.003 0.028 351 Dihedral : 4.246 18.314 309 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 15.46 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.51 (0.51), residues: 276 helix: 2.40 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.99 (0.74), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.006 0.001 TYR R 199 PHE 0.009 0.001 PHE R 282 TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 2131) covalent geometry : angle 0.45240 ( 2933) SS BOND : bond 0.00214 ( 1) SS BOND : angle 1.08135 ( 2) hydrogen bonds : bond 0.06019 ( 166) hydrogen bonds : angle 3.68234 ( 498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.050 Fit side-chains REVERT: R 40 MET cc_start: 0.7285 (mtt) cc_final: 0.7045 (mtt) REVERT: R 115 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7939 (tp) outliers start: 4 outliers final: 3 residues processed: 19 average time/residue: 0.0761 time to fit residues: 1.7242 Evaluate side-chains 19 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 0.0370 chunk 13 optimal weight: 0.0070 chunk 0 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 overall best weight: 0.2076 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.138032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.123776 restraints weight = 2885.229| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.71 r_work: 0.3353 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.002 0.015 2132 Z= 0.099 Angle : 0.414 5.382 2935 Z= 0.227 Chirality : 0.037 0.114 367 Planarity : 0.003 0.027 351 Dihedral : 3.968 18.249 309 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.55 % Allowed : 15.46 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.95 (0.52), residues: 276 helix: 2.66 (0.35), residues: 227 sheet: None (None), residues: 0 loop : -1.70 (0.80), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 63 TYR 0.007 0.001 TYR R 209 PHE 0.007 0.001 PHE R 217 TRP 0.005 0.001 TRP R 313 HIS 0.003 0.001 HIS R 93 Details of bonding type rmsd covalent geometry : bond 0.00178 ( 2131) covalent geometry : angle 0.41386 ( 2933) SS BOND : bond 0.00164 ( 1) SS BOND : angle 0.96987 ( 2) hydrogen bonds : bond 0.04203 ( 166) hydrogen bonds : angle 3.41309 ( 498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.055 Fit side-chains REVERT: R 40 MET cc_start: 0.6929 (mtt) cc_final: 0.6698 (mtt) REVERT: R 115 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7614 (tp) outliers start: 3 outliers final: 2 residues processed: 19 average time/residue: 0.0517 time to fit residues: 1.2739 Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.130169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.113853 restraints weight = 2935.623| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.81 r_work: 0.3284 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2132 Z= 0.168 Angle : 0.477 5.566 2935 Z= 0.269 Chirality : 0.039 0.126 367 Planarity : 0.003 0.028 351 Dihedral : 4.263 17.786 309 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 14.95 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.52 (0.51), residues: 276 helix: 2.42 (0.34), residues: 225 sheet: None (None), residues: 0 loop : -1.99 (0.77), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 151 TYR 0.007 0.001 TYR R 199 PHE 0.009 0.001 PHE R 290 TRP 0.006 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 2131) covalent geometry : angle 0.47666 ( 2933) SS BOND : bond 0.00238 ( 1) SS BOND : angle 1.07425 ( 2) hydrogen bonds : bond 0.06507 ( 166) hydrogen bonds : angle 3.69160 ( 498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.050 Fit side-chains REVERT: R 63 ARG cc_start: 0.4906 (ttm-80) cc_final: 0.3850 (ttm-80) REVERT: R 115 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7894 (tp) outliers start: 4 outliers final: 3 residues processed: 17 average time/residue: 0.0357 time to fit residues: 0.7862 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.127462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110863 restraints weight = 3032.068| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.86 r_work: 0.3194 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2132 Z= 0.195 Angle : 0.510 5.611 2935 Z= 0.290 Chirality : 0.040 0.132 367 Planarity : 0.003 0.028 351 Dihedral : 4.492 18.279 309 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 15.98 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.17 (0.51), residues: 276 helix: 2.16 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -2.12 (0.71), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 63 TYR 0.007 0.001 TYR R 174 PHE 0.010 0.001 PHE R 282 TRP 0.006 0.001 TRP R 109 HIS 0.005 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 2131) covalent geometry : angle 0.50931 ( 2933) SS BOND : bond 0.00229 ( 1) SS BOND : angle 1.26042 ( 2) hydrogen bonds : bond 0.07334 ( 166) hydrogen bonds : angle 3.89519 ( 498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 850.18 seconds wall clock time: 15 minutes 13.19 seconds (913.19 seconds total)