Starting phenix.real_space_refine on Fri May 9 13:59:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpf_36478/05_2025/8jpf_36478.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpf_36478/05_2025/8jpf_36478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jpf_36478/05_2025/8jpf_36478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpf_36478/05_2025/8jpf_36478.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpf_36478/05_2025/8jpf_36478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpf_36478/05_2025/8jpf_36478.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.049 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: 5 Type Number sf(0) Gaussians S 11 5.16 5 C 1481 2.51 5 N 383 2.21 5 O 393 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2269 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "R" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2178 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 3, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 123 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'SRW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.37, per 1000 atoms: 1.04 Number of scatterers: 2269 At special positions: 0 Unit cell: (48.616, 63.448, 83.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 F 1 9.00 O 393 8.00 N 383 7.00 C 1481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.65 Conformation dependent library (CDL) restraints added in 283.8 milliseconds 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 584 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 85.5% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'R' and resid 51 through 55 removed outlier: 4.267A pdb=" N LEU R 54 " --> pdb=" O SER R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 88 removed outlier: 3.772A pdb=" N VAL R 79 " --> pdb=" O VAL R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 127 removed outlier: 3.722A pdb=" N MET R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 136 through 172 removed outlier: 3.505A pdb=" N ARG R 142 " --> pdb=" O ASP R 138 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR R 145 " --> pdb=" O CYS R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 180 Processing helix chain 'R' and resid 181 through 200 Processing helix chain 'R' and resid 202 through 207 removed outlier: 3.556A pdb=" N THR R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 245 Processing helix chain 'R' and resid 245 through 271 Processing helix chain 'R' and resid 293 through 329 removed outlier: 3.991A pdb=" N VAL R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 3.530A pdb=" N ILE R 329 " --> pdb=" O MET R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 368 removed outlier: 4.026A pdb=" N MET R 347 " --> pdb=" O HIS R 343 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER R 356 " --> pdb=" O LEU R 352 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR R 358 " --> pdb=" O TYR R 354 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN R 360 " --> pdb=" O SER R 356 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 368 through 378 Processing sheet with id=AA1, first strand: chain 'R' and resid 209 through 211 193 hydrogen bonds defined for protein. 576 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: 0.60 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 372 1.33 - 1.45: 641 1.45 - 1.57: 1295 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 2324 Sorted by residual: bond pdb=" C13 SRW R 501 " pdb=" C16 SRW R 501 " ideal model delta sigma weight residual 1.447 1.290 0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" C14 SRW R 501 " pdb=" N3 SRW R 501 " ideal model delta sigma weight residual 1.309 1.453 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C13 SRW R 501 " pdb=" N1 SRW R 501 " ideal model delta sigma weight residual 1.357 1.491 -0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" C13 SRW R 501 " pdb=" N2 SRW R 501 " ideal model delta sigma weight residual 1.327 1.209 0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" C18 SRW R 501 " pdb=" N4 SRW R 501 " ideal model delta sigma weight residual 1.380 1.478 -0.098 2.00e-02 2.50e+03 2.41e+01 ... (remaining 2319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 3140 2.77 - 5.53: 41 5.53 - 8.30: 8 8.30 - 11.06: 2 11.06 - 13.83: 1 Bond angle restraints: 3192 Sorted by residual: angle pdb=" C14 SRW R 501 " pdb=" C24 SRW R 501 " pdb=" C26 SRW R 501 " ideal model delta sigma weight residual 122.08 135.91 -13.83 3.00e+00 1.11e-01 2.12e+01 angle pdb=" C ALA R 200 " pdb=" N VAL R 201 " pdb=" CA VAL R 201 " ideal model delta sigma weight residual 120.24 122.54 -2.30 6.30e-01 2.52e+00 1.33e+01 angle pdb=" C VAL R 201 " pdb=" CA VAL R 201 " pdb=" CB VAL R 201 " ideal model delta sigma weight residual 114.35 110.50 3.85 1.06e+00 8.90e-01 1.32e+01 angle pdb=" C13 SRW R 501 " pdb=" C16 SRW R 501 " pdb=" C15 SRW R 501 " ideal model delta sigma weight residual 115.31 126.05 -10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C13 SRW R 501 " pdb=" N2 SRW R 501 " pdb=" C14 SRW R 501 " ideal model delta sigma weight residual 118.85 128.84 -9.99 3.00e+00 1.11e-01 1.11e+01 ... (remaining 3187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.65: 1296 30.65 - 61.31: 50 61.31 - 91.96: 4 91.96 - 122.62: 4 122.62 - 153.27: 2 Dihedral angle restraints: 1356 sinusoidal: 458 harmonic: 898 Sorted by residual: dihedral pdb=" C25 SRW R 501 " pdb=" C24 SRW R 501 " pdb=" C26 SRW R 501 " pdb=" F1 SRW R 501 " ideal model delta sinusoidal sigma weight residual 106.02 -100.71 -153.27 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C14 SRW R 501 " pdb=" C24 SRW R 501 " pdb=" C26 SRW R 501 " pdb=" C25 SRW R 501 " ideal model delta sinusoidal sigma weight residual 110.71 -109.68 -139.61 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" C10 SRW R 501 " pdb=" C8 SRW R 501 " pdb=" C9 SRW R 501 " pdb=" C12 SRW R 501 " ideal model delta sinusoidal sigma weight residual 55.58 -60.83 116.41 1 3.00e+01 1.11e-03 1.54e+01 ... (remaining 1353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 370 0.075 - 0.150: 20 0.150 - 0.225: 1 0.225 - 0.301: 0 0.301 - 0.376: 1 Chirality restraints: 392 Sorted by residual: chirality pdb=" C24 SRW R 501 " pdb=" C14 SRW R 501 " pdb=" C25 SRW R 501 " pdb=" F1 SRW R 501 " both_signs ideal model delta sigma weight residual True 1.45 1.83 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" C8 SRW R 501 " pdb=" C12 SRW R 501 " pdb=" C3 SRW R 501 " pdb=" C9 SRW R 501 " both_signs ideal model delta sigma weight residual False -2.46 -2.66 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA VAL R 56 " pdb=" N VAL R 56 " pdb=" C VAL R 56 " pdb=" CB VAL R 56 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 389 not shown) Planarity restraints: 391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS R 132 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO R 133 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO R 133 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 133 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 165 " 0.005 2.00e-02 2.50e+03 1.05e-02 1.11e+00 pdb=" C GLU R 165 " -0.018 2.00e-02 2.50e+03 pdb=" O GLU R 165 " 0.007 2.00e-02 2.50e+03 pdb=" N ARG R 166 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 166 " 0.004 2.00e-02 2.50e+03 8.62e-03 7.43e-01 pdb=" C ARG R 166 " -0.015 2.00e-02 2.50e+03 pdb=" O ARG R 166 " 0.006 2.00e-02 2.50e+03 pdb=" N TYR R 167 " 0.005 2.00e-02 2.50e+03 ... (remaining 388 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 328 2.75 - 3.29: 2423 3.29 - 3.83: 3985 3.83 - 4.36: 4206 4.36 - 4.90: 7698 Nonbonded interactions: 18640 Sorted by model distance: nonbonded pdb=" OE1 GLU R 123 " pdb=" OH TYR R 354 " model vdw 2.214 3.040 nonbonded pdb=" OD2 ASP R 112 " pdb=" ND2 ASN R 360 " model vdw 2.347 3.120 nonbonded pdb=" OH TYR L 11 " pdb=" O LEU R 54 " model vdw 2.352 3.040 nonbonded pdb=" O GLU R 123 " pdb=" N ILE R 128 " model vdw 2.410 3.120 nonbonded pdb=" OD1 ASP R 138 " pdb=" N ALA R 139 " model vdw 2.414 3.120 ... (remaining 18635 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: 1.370 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.960 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 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 : 0.008 0.157 2324 Z= 0.401 Angle : 0.808 13.829 3192 Z= 0.383 Chirality : 0.041 0.376 392 Planarity : 0.004 0.037 391 Dihedral : 18.978 153.271 772 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.46 % Allowed : 7.34 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.48), residues: 296 helix: 2.15 (0.32), residues: 232 sheet: None (None), residues: 0 loop : -1.00 (0.78), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 134 HIS 0.003 0.001 HIS R 343 PHE 0.012 0.001 PHE R 375 TYR 0.014 0.002 TYR R 319 ARG 0.004 0.000 ARG R 148 Details of bonding type rmsd hydrogen bonds : bond 0.11551 ( 193) hydrogen bonds : angle 5.56498 ( 576) covalent geometry : bond 0.00780 ( 2324) covalent geometry : angle 0.80791 ( 3192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.246 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.2203 time to fit residues: 10.4775 Evaluate side-chains 36 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 0.0770 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN R 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.172206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.151511 restraints weight = 3520.189| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.31 r_work: 0.3781 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2324 Z= 0.136 Angle : 0.578 6.025 3192 Z= 0.304 Chirality : 0.041 0.232 392 Planarity : 0.004 0.034 391 Dihedral : 18.265 147.505 358 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.83 % Allowed : 7.80 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.48), residues: 296 helix: 2.03 (0.32), residues: 233 sheet: -3.91 (1.01), residues: 10 loop : -0.70 (0.89), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 134 HIS 0.003 0.001 HIS R 343 PHE 0.016 0.002 PHE R 375 TYR 0.019 0.002 TYR R 364 ARG 0.003 0.000 ARG R 148 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 193) hydrogen bonds : angle 4.85938 ( 576) covalent geometry : bond 0.00266 ( 2324) covalent geometry : angle 0.57751 ( 3192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: R 364 TYR cc_start: 0.8146 (m-80) cc_final: 0.7593 (m-80) outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.1733 time to fit residues: 9.6258 Evaluate side-chains 44 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 228 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN R 238 GLN R 365 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.167271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147062 restraints weight = 3585.840| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.27 r_work: 0.3745 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2324 Z= 0.145 Angle : 0.583 6.284 3192 Z= 0.301 Chirality : 0.042 0.242 392 Planarity : 0.004 0.037 391 Dihedral : 17.828 147.590 358 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.83 % Allowed : 11.01 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.48), residues: 296 helix: 1.88 (0.32), residues: 232 sheet: -3.56 (1.20), residues: 10 loop : -0.66 (0.89), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 134 HIS 0.003 0.001 HIS R 320 PHE 0.015 0.002 PHE R 353 TYR 0.015 0.002 TYR R 319 ARG 0.005 0.001 ARG L 8 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 193) hydrogen bonds : angle 4.80952 ( 576) covalent geometry : bond 0.00309 ( 2324) covalent geometry : angle 0.58340 ( 3192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: R 105 LEU cc_start: 0.8849 (mt) cc_final: 0.8645 (mt) REVERT: R 262 LYS cc_start: 0.8000 (tptt) cc_final: 0.7653 (tptm) outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.1781 time to fit residues: 9.8987 Evaluate side-chains 47 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 239 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.169079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.148914 restraints weight = 3549.488| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.25 r_work: 0.3757 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2324 Z= 0.136 Angle : 0.577 6.456 3192 Z= 0.291 Chirality : 0.041 0.292 392 Planarity : 0.004 0.039 391 Dihedral : 16.947 147.632 358 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.83 % Allowed : 12.39 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.48), residues: 296 helix: 1.89 (0.32), residues: 232 sheet: -2.89 (1.51), residues: 10 loop : -0.58 (0.91), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 134 HIS 0.003 0.001 HIS R 320 PHE 0.014 0.001 PHE R 375 TYR 0.014 0.002 TYR R 167 ARG 0.002 0.000 ARG L 8 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 193) hydrogen bonds : angle 4.71803 ( 576) covalent geometry : bond 0.00282 ( 2324) covalent geometry : angle 0.57745 ( 3192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: R 105 LEU cc_start: 0.8797 (mt) cc_final: 0.8591 (mt) REVERT: R 262 LYS cc_start: 0.8041 (tptt) cc_final: 0.7714 (tptm) outliers start: 4 outliers final: 2 residues processed: 48 average time/residue: 0.1677 time to fit residues: 9.3338 Evaluate side-chains 45 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 228 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 0.0270 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.169030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.148704 restraints weight = 3584.229| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.27 r_work: 0.3757 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2324 Z= 0.134 Angle : 0.585 6.166 3192 Z= 0.294 Chirality : 0.043 0.345 392 Planarity : 0.004 0.040 391 Dihedral : 15.789 147.505 358 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.75 % Allowed : 13.76 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.49), residues: 296 helix: 1.91 (0.32), residues: 232 sheet: -2.77 (1.59), residues: 10 loop : -0.55 (0.94), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 134 HIS 0.003 0.001 HIS R 320 PHE 0.013 0.001 PHE R 375 TYR 0.015 0.002 TYR R 167 ARG 0.005 0.001 ARG L 8 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 193) hydrogen bonds : angle 4.68500 ( 576) covalent geometry : bond 0.00277 ( 2324) covalent geometry : angle 0.58548 ( 3192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: R 105 LEU cc_start: 0.8805 (mt) cc_final: 0.8594 (mt) REVERT: R 262 LYS cc_start: 0.7959 (tptt) cc_final: 0.7644 (tptm) outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 0.1702 time to fit residues: 9.6825 Evaluate side-chains 48 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.166408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.145279 restraints weight = 3632.798| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.26 r_work: 0.3714 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2324 Z= 0.170 Angle : 0.613 6.296 3192 Z= 0.314 Chirality : 0.044 0.320 392 Planarity : 0.004 0.040 391 Dihedral : 15.605 147.596 358 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.67 % Allowed : 13.30 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.48), residues: 296 helix: 1.69 (0.32), residues: 232 sheet: -2.83 (1.60), residues: 10 loop : -0.61 (0.91), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 134 HIS 0.003 0.001 HIS R 320 PHE 0.014 0.002 PHE R 353 TYR 0.015 0.002 TYR R 167 ARG 0.001 0.000 ARG L 9 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 193) hydrogen bonds : angle 4.82864 ( 576) covalent geometry : bond 0.00383 ( 2324) covalent geometry : angle 0.61284 ( 3192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 105 LEU cc_start: 0.8834 (mt) cc_final: 0.8602 (mt) REVERT: R 262 LYS cc_start: 0.7960 (tptt) cc_final: 0.7640 (tptm) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 0.1743 time to fit residues: 9.5172 Evaluate side-chains 50 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.166347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.144954 restraints weight = 3665.384| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.29 r_work: 0.3709 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2324 Z= 0.168 Angle : 0.622 6.582 3192 Z= 0.316 Chirality : 0.044 0.325 392 Planarity : 0.004 0.041 391 Dihedral : 15.563 147.451 358 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.67 % Allowed : 13.76 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.48), residues: 296 helix: 1.61 (0.32), residues: 232 sheet: -2.39 (1.73), residues: 10 loop : -0.61 (0.92), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 134 HIS 0.003 0.001 HIS R 320 PHE 0.014 0.002 PHE R 353 TYR 0.016 0.002 TYR R 167 ARG 0.002 0.000 ARG L 8 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 193) hydrogen bonds : angle 4.86748 ( 576) covalent geometry : bond 0.00379 ( 2324) covalent geometry : angle 0.62178 ( 3192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 105 LEU cc_start: 0.8830 (mt) cc_final: 0.8598 (mt) REVERT: R 262 LYS cc_start: 0.7954 (tptt) cc_final: 0.7632 (tptm) REVERT: R 359 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8150 (tt) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 0.1691 time to fit residues: 9.1906 Evaluate side-chains 51 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.166229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144660 restraints weight = 3702.533| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.31 r_work: 0.3703 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2324 Z= 0.166 Angle : 0.623 7.119 3192 Z= 0.316 Chirality : 0.043 0.324 392 Planarity : 0.004 0.041 391 Dihedral : 15.527 147.480 358 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.67 % Allowed : 13.30 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.48), residues: 296 helix: 1.59 (0.32), residues: 232 sheet: -2.35 (1.72), residues: 10 loop : -0.68 (0.92), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 134 HIS 0.003 0.001 HIS R 320 PHE 0.014 0.002 PHE R 375 TYR 0.017 0.002 TYR R 167 ARG 0.002 0.000 ARG R 148 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 193) hydrogen bonds : angle 4.87645 ( 576) covalent geometry : bond 0.00372 ( 2324) covalent geometry : angle 0.62301 ( 3192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 105 LEU cc_start: 0.8825 (mt) cc_final: 0.8584 (mt) REVERT: R 262 LYS cc_start: 0.7963 (tptt) cc_final: 0.7641 (tptm) outliers start: 8 outliers final: 7 residues processed: 49 average time/residue: 0.1677 time to fit residues: 9.5708 Evaluate side-chains 51 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.168823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.147846 restraints weight = 3563.691| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.29 r_work: 0.3746 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2324 Z= 0.139 Angle : 0.607 8.227 3192 Z= 0.305 Chirality : 0.042 0.327 392 Planarity : 0.004 0.042 391 Dihedral : 15.327 147.494 358 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.29 % Allowed : 14.68 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.48), residues: 296 helix: 1.71 (0.32), residues: 232 sheet: -2.11 (1.80), residues: 10 loop : -0.56 (0.94), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 134 HIS 0.002 0.001 HIS R 320 PHE 0.012 0.001 PHE R 375 TYR 0.018 0.002 TYR R 167 ARG 0.002 0.000 ARG R 148 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 193) hydrogen bonds : angle 4.81918 ( 576) covalent geometry : bond 0.00288 ( 2324) covalent geometry : angle 0.60651 ( 3192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 105 LEU cc_start: 0.8802 (mt) cc_final: 0.8560 (mt) REVERT: R 262 LYS cc_start: 0.7975 (tptt) cc_final: 0.7647 (tptm) outliers start: 5 outliers final: 4 residues processed: 46 average time/residue: 0.1794 time to fit residues: 9.6047 Evaluate side-chains 48 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.169716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.148023 restraints weight = 3592.509| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.37 r_work: 0.3738 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2324 Z= 0.140 Angle : 0.624 8.180 3192 Z= 0.310 Chirality : 0.043 0.329 392 Planarity : 0.004 0.042 391 Dihedral : 15.272 147.499 358 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.83 % Allowed : 16.06 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.48), residues: 296 helix: 1.72 (0.32), residues: 232 sheet: -1.88 (1.86), residues: 10 loop : -0.48 (0.96), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 134 HIS 0.002 0.001 HIS R 320 PHE 0.012 0.001 PHE R 375 TYR 0.018 0.002 TYR R 167 ARG 0.002 0.000 ARG R 148 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 193) hydrogen bonds : angle 4.82226 ( 576) covalent geometry : bond 0.00294 ( 2324) covalent geometry : angle 0.62412 ( 3192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 70 TYR cc_start: 0.8239 (m-80) cc_final: 0.8016 (m-80) REVERT: R 105 LEU cc_start: 0.8793 (mt) cc_final: 0.8557 (mt) REVERT: R 175 LYS cc_start: 0.6886 (pttm) cc_final: 0.6625 (pttm) REVERT: R 262 LYS cc_start: 0.7912 (tptt) cc_final: 0.7601 (tptm) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.1703 time to fit residues: 9.2799 Evaluate side-chains 48 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.0270 chunk 1 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.169694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.148942 restraints weight = 3515.718| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.27 r_work: 0.3746 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2324 Z= 0.138 Angle : 0.638 13.224 3192 Z= 0.310 Chirality : 0.042 0.331 392 Planarity : 0.004 0.042 391 Dihedral : 15.220 147.527 358 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.29 % Allowed : 16.51 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.48), residues: 296 helix: 1.77 (0.32), residues: 232 sheet: -1.69 (1.92), residues: 10 loop : -0.48 (0.95), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 134 HIS 0.002 0.001 HIS R 343 PHE 0.011 0.001 PHE R 375 TYR 0.017 0.002 TYR R 167 ARG 0.002 0.000 ARG R 148 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 193) hydrogen bonds : angle 4.75269 ( 576) covalent geometry : bond 0.00288 ( 2324) covalent geometry : angle 0.63753 ( 3192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1438.79 seconds wall clock time: 25 minutes 42.21 seconds (1542.21 seconds total)