Starting phenix.real_space_refine on Tue Aug 4 11:46:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v4d_64777/08_2026/9v4d_64777.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v4d_64777/08_2026/9v4d_64777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v4d_64777/08_2026/9v4d_64777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v4d_64777/08_2026/9v4d_64777.map" model { file = "/net/cci-nas-00/data/ceres_data/9v4d_64777/08_2026/9v4d_64777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v4d_64777/08_2026/9v4d_64777.cif" } resolution = 3.07 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= 0.001 sd= 0.016 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 15 5.16 5 C 1349 2.51 5 N 346 2.21 5 O 328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2038 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1969 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 250} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 51 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 4} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Classifications: {'peptide': 2} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 1} Time building chain proxies: 1.22, per 1000 atoms: 0.60 Number of scatterers: 2038 At special positions: 0 Unit cell: (52.0149, 55.335, 83.0025, 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 15 16.00 O 328 8.00 N 346 7.00 C 1349 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 219 " 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 Links applied TRANS " DAL C 7 " - " LEU C 6 " Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 112.4 milliseconds 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL C 7 " Number of C-beta restraints generated: 506 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 1 sheets defined 80.7% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 37 through 64 Proline residue: A 51 - end of helix Processing helix chain 'A' and resid 65 through 66 No H-bonds generated for 'chain 'A' and resid 65 through 66' Processing helix chain 'A' and resid 67 through 68 No H-bonds generated for 'chain 'A' and resid 67 through 68' Processing helix chain 'A' and resid 69 through 96 removed outlier: 4.019A pdb=" N LEU A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 87 " --> pdb=" O CYS A 83 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.724A pdb=" N VAL A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 102 through 138 Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 143 through 172 removed outlier: 3.866A pdb=" N GLY A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 193 through 209 Processing helix chain 'A' and resid 209 through 225 Processing helix chain 'A' and resid 233 through 259 removed outlier: 3.596A pdb=" N ILE A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 263 through 295 Proline residue: A 274 - end of helix removed outlier: 4.103A pdb=" N HIS A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N SER A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Proline residue: A 288 - end of helix removed outlier: 4.078A pdb=" N TYR A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 177 153 hydrogen bonds defined for protein. 459 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.54 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 297 1.31 - 1.44: 580 1.44 - 1.56: 1198 1.56 - 1.69: 1 1.69 - 1.81: 18 Bond restraints: 2094 Sorted by residual: bond pdb=" C MET A 289 " pdb=" N LEU A 290 " ideal model delta sigma weight residual 1.332 1.430 -0.098 1.29e-02 6.01e+03 5.79e+01 bond pdb=" C ACE C 0 " pdb=" CH3 ACE C 0 " ideal model delta sigma weight residual 1.506 1.565 -0.059 2.00e-02 2.50e+03 8.83e+00 bond pdb=" N LEU C 4 " pdb=" CA LEU C 4 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.25e-02 6.40e+03 6.85e+00 bond pdb=" N GLY C 5 " pdb=" CA GLY C 5 " ideal model delta sigma weight residual 1.447 1.478 -0.030 1.23e-02 6.61e+03 6.10e+00 bond pdb=" N PHE A 291 " pdb=" CA PHE A 291 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.84e+00 ... (remaining 2089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 2811 2.20 - 4.40: 46 4.40 - 6.60: 16 6.60 - 8.80: 0 8.80 - 10.99: 2 Bond angle restraints: 2875 Sorted by residual: angle pdb=" CH3 ACE C 0 " pdb=" C ACE C 0 " pdb=" N TYR C 1 " ideal model delta sigma weight residual 116.20 127.19 -10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CA GLY C 5 " pdb=" C GLY C 5 " pdb=" O GLY C 5 " ideal model delta sigma weight residual 121.92 118.09 3.83 1.05e+00 9.07e-01 1.33e+01 angle pdb=" O ACE C 0 " pdb=" C ACE C 0 " pdb=" CH3 ACE C 0 " ideal model delta sigma weight residual 123.82 113.32 10.50 3.00e+00 1.11e-01 1.23e+01 angle pdb=" CA LEU C 4 " pdb=" C LEU C 4 " pdb=" O LEU C 4 " ideal model delta sigma weight residual 121.44 117.71 3.73 1.08e+00 8.57e-01 1.19e+01 angle pdb=" CA MET A 289 " pdb=" C MET A 289 " pdb=" N LEU A 290 " ideal model delta sigma weight residual 116.84 112.01 4.83 1.71e+00 3.42e-01 7.97e+00 ... (remaining 2870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 1069 15.75 - 31.50: 108 31.50 - 47.25: 29 47.25 - 63.00: 6 63.00 - 78.75: 1 Dihedral angle restraints: 1213 sinusoidal: 425 harmonic: 788 Sorted by residual: dihedral pdb=" CB MET A 118 " pdb=" CG MET A 118 " pdb=" SD MET A 118 " pdb=" CE MET A 118 " ideal model delta sinusoidal sigma weight residual 60.00 116.52 -56.52 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CG ARG A 268 " pdb=" CD ARG A 268 " pdb=" NE ARG A 268 " pdb=" CZ ARG A 268 " ideal model delta sinusoidal sigma weight residual 180.00 138.96 41.04 2 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" CB MET A 289 " pdb=" CG MET A 289 " pdb=" SD MET A 289 " pdb=" CE MET A 289 " ideal model delta sinusoidal sigma weight residual -60.00 -8.99 -51.01 3 1.50e+01 4.44e-03 8.97e+00 ... (remaining 1210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 190 0.023 - 0.046: 90 0.046 - 0.070: 36 0.070 - 0.093: 17 0.093 - 0.116: 15 Chirality restraints: 348 Sorted by residual: chirality pdb=" CA PRO A 38 " pdb=" N PRO A 38 " pdb=" C PRO A 38 " pdb=" CB PRO A 38 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA GLU A 273 " pdb=" N GLU A 273 " pdb=" C GLU A 273 " pdb=" CB GLU A 273 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.27e-01 chirality pdb=" CA VAL A 188 " pdb=" N VAL A 188 " pdb=" C VAL A 188 " pdb=" CB VAL A 188 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.98e-01 ... (remaining 345 not shown) Planarity restraints: 353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 289 " 0.027 2.00e-02 2.50e+03 5.62e-02 3.15e+01 pdb=" C MET A 289 " -0.097 2.00e-02 2.50e+03 pdb=" O MET A 289 " 0.039 2.00e-02 2.50e+03 pdb=" N LEU A 290 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 180 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO A 181 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 167 " 0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO A 168 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " 0.029 5.00e-02 4.00e+02 ... (remaining 350 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 497 2.80 - 3.33: 2011 3.33 - 3.85: 3490 3.85 - 4.38: 3684 4.38 - 4.90: 6668 Nonbonded interactions: 16350 Sorted by model distance: nonbonded pdb=" OG1 THR A 201 " pdb=" OG1 THR A 257 " model vdw 2.279 3.040 nonbonded pdb=" NE2 GLN A 177 " pdb=" O GLU A 178 " model vdw 2.371 3.120 nonbonded pdb=" O GLY A 49 " pdb=" ND2 ASN A 53 " model vdw 2.388 3.120 nonbonded pdb=" O SER A 112 " pdb=" OG1 THR A 166 " model vdw 2.497 3.040 nonbonded pdb=" O ILE A 89 " pdb=" OH TYR A 102 " model vdw 2.552 3.040 ... (remaining 16345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 6.220 Find NCS groups from input model: 0.010 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 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 0.098 2097 Z= 0.259 Angle : 0.756 10.994 2882 Z= 0.379 Chirality : 0.038 0.116 348 Planarity : 0.007 0.060 352 Dihedral : 14.247 78.753 698 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.50 % Allowed : 18.81 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: 2.36 (0.57), residues: 269 helix: 2.27 (0.38), residues: 209 sheet: -2.24 (1.41), residues: 12 loop : -0.59 (1.10), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 232 TYR 0.008 0.001 TYR C 1 PHE 0.005 0.001 PHE A 46 TRP 0.007 0.001 TRP A 72 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.26 ( 2094) covalent geometry : angle 0.75037 / 0.38 ( 2875) SS BOND : bond 0.00062 / 0.03 ( 2) SS BOND : angle 1.75098 / 0.58 ( 4) hydrogen bonds : bond 0.09646 / 7.16 ( 153) hydrogen bonds : angle 5.75522 / 4.64 ( 459) link_TRANS : bond 0.00308 / 0.16 ( 1) link_TRANS : angle 2.21629 / 0.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.080 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.0646 time to fit residues: 1.5628 Evaluate side-chains 19 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.148758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.112013 restraints weight = 2334.903| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.59 r_work: 0.3081 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2097 Z= 0.155 Angle : 0.661 5.350 2882 Z= 0.320 Chirality : 0.040 0.132 348 Planarity : 0.006 0.045 352 Dihedral : 5.867 56.791 299 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.47 % Allowed : 15.35 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: 2.38 (0.55), residues: 269 helix: 2.22 (0.37), residues: 213 sheet: -2.25 (1.38), residues: 12 loop : -0.46 (1.05), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 173 TYR 0.009 0.001 TYR A 42 PHE 0.007 0.001 PHE A 46 TRP 0.008 0.001 TRP A 72 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 2094) covalent geometry : angle 0.65756 / 0.32 ( 2875) SS BOND : bond 0.00099 / 0.05 ( 2) SS BOND : angle 2.01019 / 0.67 ( 4) hydrogen bonds : bond 0.04464 / 3.07 ( 153) hydrogen bonds : angle 5.24706 / 4.19 ( 459) link_TRANS : bond 0.00359 / 0.19 ( 1) link_TRANS : angle 0.65987 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.072 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 25 average time/residue: 0.0467 time to fit residues: 1.4845 Evaluate side-chains 24 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain C residue 6 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.147684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.110771 restraints weight = 2356.874| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.57 r_work: 0.3044 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2097 Z= 0.170 Angle : 0.669 6.078 2882 Z= 0.324 Chirality : 0.041 0.140 348 Planarity : 0.006 0.044 352 Dihedral : 5.661 50.383 299 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.45 % Allowed : 13.86 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: 2.29 (0.55), residues: 269 helix: 2.19 (0.37), residues: 212 sheet: -2.32 (1.37), residues: 12 loop : -0.63 (1.02), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.007 0.002 TYR C 1 PHE 0.009 0.001 PHE A 46 TRP 0.008 0.001 TRP A 72 HIS 0.005 0.002 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 2094) covalent geometry : angle 0.66363 / 0.32 ( 2875) SS BOND : bond 0.00191 / 0.09 ( 2) SS BOND : angle 2.35508 / 0.84 ( 4) hydrogen bonds : bond 0.04679 / 3.19 ( 153) hydrogen bonds : angle 5.13814 / 4.05 ( 459) link_TRANS : bond 0.00279 / 0.15 ( 1) link_TRANS : angle 0.62325 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.069 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 28 average time/residue: 0.0442 time to fit residues: 1.5462 Evaluate side-chains 29 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain C residue 6 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.0670 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.149900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.113105 restraints weight = 2332.384| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.56 r_work: 0.3053 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2097 Z= 0.137 Angle : 0.612 5.346 2882 Z= 0.298 Chirality : 0.038 0.132 348 Planarity : 0.006 0.041 352 Dihedral : 5.472 46.175 299 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.96 % Allowed : 14.85 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: 2.51 (0.55), residues: 269 helix: 2.31 (0.37), residues: 213 sheet: -2.69 (1.28), residues: 12 loop : -0.24 (1.05), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 204 TYR 0.007 0.001 TYR C 1 PHE 0.009 0.001 PHE A 46 TRP 0.007 0.001 TRP A 72 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 2094) covalent geometry : angle 0.60796 / 0.30 ( 2875) SS BOND : bond 0.00167 / 0.08 ( 2) SS BOND : angle 2.04764 / 0.69 ( 4) hydrogen bonds : bond 0.04091 / 2.78 ( 153) hydrogen bonds : angle 4.98296 / 3.91 ( 459) link_TRANS : bond 0.00283 / 0.15 ( 1) link_TRANS : angle 0.74646 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.073 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 27 average time/residue: 0.0467 time to fit residues: 1.5961 Evaluate side-chains 27 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain C residue 6 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.148610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.111965 restraints weight = 2318.115| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.56 r_work: 0.3028 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2097 Z= 0.160 Angle : 0.647 5.986 2882 Z= 0.313 Chirality : 0.040 0.133 348 Planarity : 0.006 0.041 352 Dihedral : 5.345 40.901 299 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.95 % Allowed : 14.36 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: 2.31 (0.55), residues: 269 helix: 2.18 (0.37), residues: 213 sheet: -2.79 (1.30), residues: 12 loop : -0.37 (1.03), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 183 TYR 0.007 0.001 TYR C 1 PHE 0.009 0.001 PHE A 46 TRP 0.007 0.001 TRP A 72 HIS 0.005 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 2094) covalent geometry : angle 0.64128 / 0.31 ( 2875) SS BOND : bond 0.00211 / 0.10 ( 2) SS BOND : angle 2.33519 / 0.82 ( 4) hydrogen bonds : bond 0.04508 / 3.07 ( 153) hydrogen bonds : angle 4.99657 / 3.92 ( 459) link_TRANS : bond 0.00282 / 0.15 ( 1) link_TRANS : angle 0.67574 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.042 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 27 average time/residue: 0.0401 time to fit residues: 1.3810 Evaluate side-chains 28 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain C residue 6 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 7 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.150275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.114146 restraints weight = 2273.866| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.51 r_work: 0.3058 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2097 Z= 0.139 Angle : 0.609 5.421 2882 Z= 0.296 Chirality : 0.038 0.128 348 Planarity : 0.005 0.040 352 Dihedral : 5.182 39.326 299 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.45 % Allowed : 13.37 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: 2.44 (0.55), residues: 269 helix: 2.28 (0.37), residues: 213 sheet: -2.88 (1.26), residues: 12 loop : -0.32 (1.04), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 183 TYR 0.008 0.001 TYR C 1 PHE 0.009 0.001 PHE A 46 TRP 0.007 0.001 TRP A 72 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 2094) covalent geometry : angle 0.60437 / 0.29 ( 2875) SS BOND : bond 0.00202 / 0.10 ( 2) SS BOND : angle 2.16292 / 0.74 ( 4) hydrogen bonds : bond 0.04117 / 2.79 ( 153) hydrogen bonds : angle 4.91840 / 3.85 ( 459) link_TRANS : bond 0.00284 / 0.15 ( 1) link_TRANS : angle 0.75141 / 0.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.071 Fit side-chains REVERT: A 55 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6639 (mtt) outliers start: 11 outliers final: 7 residues processed: 27 average time/residue: 0.0460 time to fit residues: 1.5681 Evaluate side-chains 28 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain C residue 6 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.148789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.113637 restraints weight = 2301.831| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.88 r_work: 0.3011 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2097 Z= 0.162 Angle : 0.646 5.987 2882 Z= 0.312 Chirality : 0.040 0.134 348 Planarity : 0.005 0.040 352 Dihedral : 5.102 38.880 299 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.45 % Allowed : 12.87 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: 2.29 (0.55), residues: 269 helix: 2.17 (0.37), residues: 213 sheet: -2.88 (1.30), residues: 12 loop : -0.39 (1.03), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 183 TYR 0.007 0.001 TYR A 119 PHE 0.010 0.001 PHE A 46 TRP 0.007 0.001 TRP A 72 HIS 0.005 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 ( 2094) covalent geometry : angle 0.64019 / 0.31 ( 2875) SS BOND : bond 0.00221 / 0.11 ( 2) SS BOND : angle 2.36887 / 0.83 ( 4) hydrogen bonds : bond 0.04487 / 3.06 ( 153) hydrogen bonds : angle 4.95929 / 3.88 ( 459) link_TRANS : bond 0.00280 / 0.15 ( 1) link_TRANS : angle 0.68283 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.047 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 29 average time/residue: 0.0417 time to fit residues: 1.5516 Evaluate side-chains 29 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain C residue 6 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 10 optimal weight: 0.2980 chunk 19 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.150399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.113287 restraints weight = 2327.938| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.57 r_work: 0.3041 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2097 Z= 0.139 Angle : 0.611 5.451 2882 Z= 0.295 Chirality : 0.039 0.127 348 Planarity : 0.005 0.039 352 Dihedral : 4.992 37.908 299 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.96 % Allowed : 14.85 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: 2.42 (0.55), residues: 269 helix: 2.28 (0.37), residues: 213 sheet: -2.94 (1.26), residues: 12 loop : -0.40 (1.03), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 204 TYR 0.007 0.001 TYR C 1 PHE 0.009 0.001 PHE A 46 TRP 0.007 0.001 TRP A 72 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 2094) covalent geometry : angle 0.60538 / 0.29 ( 2875) SS BOND : bond 0.00203 / 0.10 ( 2) SS BOND : angle 2.17712 / 0.75 ( 4) hydrogen bonds : bond 0.04129 / 2.80 ( 153) hydrogen bonds : angle 4.88858 / 3.82 ( 459) link_TRANS : bond 0.00294 / 0.15 ( 1) link_TRANS : angle 0.77093 / 0.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.069 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 27 average time/residue: 0.0452 time to fit residues: 1.5453 Evaluate side-chains 28 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 285 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.0470 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.150183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.113705 restraints weight = 2295.602| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.53 r_work: 0.3034 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2097 Z= 0.143 Angle : 0.616 5.613 2882 Z= 0.298 Chirality : 0.039 0.129 348 Planarity : 0.005 0.039 352 Dihedral : 4.117 26.459 297 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.96 % Allowed : 14.85 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: 2.41 (0.55), residues: 269 helix: 2.33 (0.37), residues: 210 sheet: -3.00 (1.24), residues: 12 loop : -0.54 (1.00), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 183 TYR 0.007 0.001 TYR C 1 PHE 0.009 0.001 PHE A 46 TRP 0.007 0.001 TRP A 72 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 2094) covalent geometry : angle 0.61074 / 0.30 ( 2875) SS BOND : bond 0.00218 / 0.10 ( 2) SS BOND : angle 2.21571 / 0.76 ( 4) hydrogen bonds : bond 0.04185 / 2.84 ( 153) hydrogen bonds : angle 4.89285 / 3.83 ( 459) link_TRANS : bond 0.00305 / 0.16 ( 1) link_TRANS : angle 0.75187 / 0.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.068 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 27 average time/residue: 0.0448 time to fit residues: 1.5381 Evaluate side-chains 28 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 285 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 0.0050 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.0030 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.151672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.115326 restraints weight = 2352.147| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.52 r_work: 0.3060 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2097 Z= 0.126 Angle : 0.588 5.456 2882 Z= 0.284 Chirality : 0.038 0.126 348 Planarity : 0.005 0.038 352 Dihedral : 4.065 24.609 297 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.47 % Allowed : 15.35 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: 2.58 (0.56), residues: 269 helix: 2.46 (0.38), residues: 210 sheet: -3.00 (1.23), residues: 12 loop : -0.50 (1.02), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 204 TYR 0.008 0.001 TYR C 1 PHE 0.009 0.001 PHE A 46 TRP 0.006 0.001 TRP A 72 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 2094) covalent geometry : angle 0.58341 / 0.28 ( 2875) SS BOND : bond 0.00185 / 0.09 ( 2) SS BOND : angle 2.02731 / 0.69 ( 4) hydrogen bonds : bond 0.03855 / 2.61 ( 153) hydrogen bonds : angle 4.81604 / 3.76 ( 459) link_TRANS : bond 0.00300 / 0.16 ( 1) link_TRANS : angle 0.77867 / 0.28 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.042 Fit side-chains REVERT: A 152 GLN cc_start: 0.7209 (pt0) cc_final: 0.6930 (mt0) outliers start: 7 outliers final: 5 residues processed: 26 average time/residue: 0.0297 time to fit residues: 0.9767 Evaluate side-chains 27 residues out of total 208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 285 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.149706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.111893 restraints weight = 2349.607| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.61 r_work: 0.3014 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2097 Z= 0.154 Angle : 0.630 5.917 2882 Z= 0.304 Chirality : 0.039 0.128 348 Planarity : 0.005 0.039 352 Dihedral : 4.082 24.811 297 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.48 % Allowed : 15.84 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 are not related in a simple way. whole: 2.36 (0.55), residues: 269 helix: 2.30 (0.37), residues: 210 sheet: -2.97 (1.26), residues: 12 loop : -0.57 (1.01), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 183 TYR 0.006 0.001 TYR A 119 PHE 0.009 0.001 PHE A 46 TRP 0.007 0.001 TRP A 72 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 ( 2094) covalent geometry : angle 0.62452 / 0.30 ( 2875) SS BOND : bond 0.00239 / 0.12 ( 2) SS BOND : angle 2.27916 / 0.79 ( 4) hydrogen bonds : bond 0.04329 / 2.95 ( 153) hydrogen bonds : angle 4.88387 / 3.82 ( 459) link_TRANS : bond 0.00294 / 0.15 ( 1) link_TRANS : angle 0.74935 / 0.26 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 774.61 seconds wall clock time: 14 minutes 8.33 seconds (848.33 seconds total)