Starting phenix.real_space_refine on Tue Feb 11 06:01:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iy6_35815/02_2025/8iy6_35815.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iy6_35815/02_2025/8iy6_35815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iy6_35815/02_2025/8iy6_35815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iy6_35815/02_2025/8iy6_35815.map" model { file = "/net/cci-nas-00/data/ceres_data/8iy6_35815/02_2025/8iy6_35815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iy6_35815/02_2025/8iy6_35815.cif" } resolution = 3.13 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 ------------------------------------------------------------------------------- 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= -0.041 sd= 0.433 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2297 atoms to isotropic. 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 29 5.16 5 C 1650 2.51 5 N 395 2.21 5 O 421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2495 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 293, 2321 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 293, 2321 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2371 Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 171 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Time building chain proxies: 3.06, per 1000 atoms: 1.23 Number of scatterers: 2495 At special positions: 0 Unit cell: (66.234, 67.396, 80.178, 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 29 16.00 O 421 8.00 N 395 7.00 C 1650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.03 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 255 " distance=2.03 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 15 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 11 " distance=2.04 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: 0.60 Conformation dependent library (CDL) restraints added in 556.8 milliseconds 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 610 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 82.5% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 97 through 129 Processing helix chain 'R' and resid 130 through 133 Processing helix chain 'R' and resid 134 through 165 Proline residue: R 156 - end of helix Processing helix chain 'R' and resid 170 through 205 removed outlier: 3.686A pdb=" N CYS R 174 " --> pdb=" O GLY R 170 " (cutoff:3.500A) Proline residue: R 178 - end of helix Processing helix chain 'R' and resid 219 through 233 Processing helix chain 'R' and resid 233 through 239 Processing helix chain 'R' and resid 263 through 281 removed outlier: 6.312A pdb=" N ASP R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TRP R 275 " --> pdb=" O THR R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 303 Processing helix chain 'R' and resid 319 through 350 Proline residue: R 338 - end of helix Processing helix chain 'R' and resid 357 through 390 removed outlier: 3.703A pdb=" N VAL R 366 " --> pdb=" O SER R 362 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN R 382 " --> pdb=" O ASN R 378 " (cutoff:3.500A) Proline residue: R 383 - end of helix Processing helix chain 'R' and resid 390 through 403 removed outlier: 3.584A pdb=" N CYS R 403 " --> pdb=" O SER R 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 18 Processing sheet with id=AA1, first strand: chain 'R' and resid 240 through 247 202 hydrogen bonds defined for protein. 599 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: 0.68 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 744 1.34 - 1.46: 622 1.46 - 1.58: 1151 1.58 - 1.70: 0 1.70 - 1.82: 37 Bond restraints: 2554 Sorted by residual: bond pdb=" N CYS L 1 " pdb=" CA CYS L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" CB ASN R 353 " pdb=" CG ASN R 353 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.34e-01 bond pdb=" CA ASN R 353 " pdb=" CB ASN R 353 " ideal model delta sigma weight residual 1.541 1.549 -0.008 1.20e-02 6.94e+03 4.07e-01 bond pdb=" CD LYS R 175 " pdb=" CE LYS R 175 " ideal model delta sigma weight residual 1.520 1.502 0.018 3.00e-02 1.11e+03 3.46e-01 bond pdb=" CG PRO R 136 " pdb=" CD PRO R 136 " ideal model delta sigma weight residual 1.503 1.486 0.017 3.40e-02 8.65e+02 2.41e-01 ... (remaining 2549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 3234 0.95 - 1.91: 200 1.91 - 2.86: 24 2.86 - 3.82: 6 3.82 - 4.77: 10 Bond angle restraints: 3474 Sorted by residual: angle pdb=" N ILE R 238 " pdb=" CA ILE R 238 " pdb=" C ILE R 238 " ideal model delta sigma weight residual 113.47 109.23 4.24 1.01e+00 9.80e-01 1.77e+01 angle pdb=" N ILE R 381 " pdb=" CA ILE R 381 " pdb=" C ILE R 381 " ideal model delta sigma weight residual 110.62 112.83 -2.21 1.02e+00 9.61e-01 4.69e+00 angle pdb=" CA ILE R 238 " pdb=" C ILE R 238 " pdb=" O ILE R 238 " ideal model delta sigma weight residual 118.98 120.65 -1.67 9.00e-01 1.23e+00 3.43e+00 angle pdb=" CA ASN R 353 " pdb=" CB ASN R 353 " pdb=" CG ASN R 353 " ideal model delta sigma weight residual 112.60 114.38 -1.78 1.00e+00 1.00e+00 3.16e+00 angle pdb=" N ASN R 353 " pdb=" CA ASN R 353 " pdb=" CB ASN R 353 " ideal model delta sigma weight residual 114.17 112.18 1.99 1.14e+00 7.69e-01 3.04e+00 ... (remaining 3469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 1367 15.65 - 31.29: 134 31.29 - 46.93: 25 46.93 - 62.58: 3 62.58 - 78.22: 3 Dihedral angle restraints: 1532 sinusoidal: 597 harmonic: 935 Sorted by residual: dihedral pdb=" CB CYS R 90 " pdb=" SG CYS R 90 " pdb=" SG CYS R 358 " pdb=" CB CYS R 358 " ideal model delta sinusoidal sigma weight residual 93.00 45.46 47.54 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CA MET R 245 " pdb=" C MET R 245 " pdb=" N ASP R 246 " pdb=" CA ASP R 246 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" SG CYS L 1 " pdb=" CB CYS L 15 " pdb=" SG CYS L 15 " pdb=" CA CYS L 15 " ideal model delta sinusoidal sigma weight residual 79.00 3.83 75.17 1 2.00e+01 2.50e-03 1.79e+01 ... (remaining 1529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 291 0.030 - 0.061: 80 0.061 - 0.091: 35 0.091 - 0.121: 10 0.121 - 0.152: 2 Chirality restraints: 418 Sorted by residual: chirality pdb=" CA ILE R 254 " pdb=" N ILE R 254 " pdb=" C ILE R 254 " pdb=" CB ILE R 254 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE R 94 " pdb=" N ILE R 94 " pdb=" C ILE R 94 " pdb=" CB ILE R 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE R 96 " pdb=" N ILE R 96 " pdb=" C ILE R 96 " pdb=" CB ILE R 96 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 415 not shown) Planarity restraints: 416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN R 353 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C ASN R 353 " -0.032 2.00e-02 2.50e+03 pdb=" O ASN R 353 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP R 354 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 92 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO R 93 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO R 93 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 93 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 112 " -0.010 2.00e-02 2.50e+03 7.22e-03 9.13e-01 pdb=" CG PHE R 112 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE R 112 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 112 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE R 112 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 112 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 112 " -0.005 2.00e-02 2.50e+03 ... (remaining 413 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 74 2.71 - 3.26: 2685 3.26 - 3.81: 4148 3.81 - 4.35: 4868 4.35 - 4.90: 8375 Nonbonded interactions: 20150 Sorted by model distance: nonbonded pdb=" OG SER R 342 " pdb=" OD1 ASP R 368 " model vdw 2.168 3.040 nonbonded pdb=" O ASN R 353 " pdb=" OD1 ASN R 353 " model vdw 2.231 3.040 nonbonded pdb=" NZ LYS R 161 " pdb=" O ASP L 18 " model vdw 2.293 3.120 nonbonded pdb=" OG SER R 108 " pdb=" OD1 ASN R 373 " model vdw 2.354 3.040 nonbonded pdb=" O ASP R 354 " pdb=" NH1 ARG R 357 " model vdw 2.363 3.120 ... (remaining 20145 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=0.30 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: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.170 Find NCS groups from input model: 0.030 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 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 : 0.003 0.033 2554 Z= 0.170 Angle : 0.545 4.771 3474 Z= 0.308 Chirality : 0.036 0.152 418 Planarity : 0.004 0.043 416 Dihedral : 12.047 78.223 910 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 307 helix: 1.90 (0.33), residues: 242 sheet: -1.52 (1.40), residues: 10 loop : -1.31 (0.79), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 276 HIS 0.003 0.001 HIS R 258 PHE 0.015 0.001 PHE R 112 TYR 0.007 0.001 TYR R 200 ARG 0.003 0.000 ARG R 343 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.286 Fit side-chains REVERT: R 133 ARG cc_start: 0.6820 (tmm-80) cc_final: 0.6597 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1920 time to fit residues: 12.7845 Evaluate side-chains 46 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.222388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.203048 restraints weight = 9779.495| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 3.31 r_work: 0.3991 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3985 r_free = 0.3985 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3985 r_free = 0.3985 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2554 Z= 0.258 Angle : 0.693 7.801 3474 Z= 0.358 Chirality : 0.045 0.255 418 Planarity : 0.005 0.044 416 Dihedral : 4.688 22.600 337 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.42 % Allowed : 8.51 % Favored : 90.07 % 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: 1.58 (0.47), residues: 307 helix: 1.62 (0.32), residues: 245 sheet: -1.30 (1.39), residues: 10 loop : -1.07 (0.92), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 276 HIS 0.006 0.002 HIS R 258 PHE 0.028 0.003 PHE R 100 TYR 0.010 0.002 TYR R 350 ARG 0.006 0.001 ARG R 343 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.259 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.2237 time to fit residues: 12.8657 Evaluate side-chains 47 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 14 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.225979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.210439 restraints weight = 5401.624| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 2.17 r_work: 0.4104 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2554 Z= 0.168 Angle : 0.602 8.508 3474 Z= 0.309 Chirality : 0.041 0.233 418 Planarity : 0.004 0.039 416 Dihedral : 4.486 21.216 337 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.06 % Allowed : 11.35 % Favored : 87.59 % 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: 2.10 (0.48), residues: 307 helix: 2.02 (0.32), residues: 244 sheet: -1.03 (1.36), residues: 10 loop : -1.11 (0.92), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 276 HIS 0.003 0.001 HIS R 258 PHE 0.029 0.002 PHE R 100 TYR 0.008 0.001 TYR R 350 ARG 0.005 0.001 ARG R 343 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.271 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.1947 time to fit residues: 10.8343 Evaluate side-chains 47 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 365 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.222708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.205850 restraints weight = 6370.940| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.50 r_work: 0.4051 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4056 r_free = 0.4056 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4056 r_free = 0.4056 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2554 Z= 0.231 Angle : 0.636 6.970 3474 Z= 0.328 Chirality : 0.043 0.284 418 Planarity : 0.005 0.040 416 Dihedral : 4.555 21.046 337 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.77 % Allowed : 10.99 % Favored : 87.23 % 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 (0.48), residues: 307 helix: 1.90 (0.32), residues: 244 sheet: -0.78 (1.34), residues: 10 loop : -1.18 (0.95), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 276 HIS 0.005 0.001 HIS R 258 PHE 0.027 0.003 PHE R 100 TYR 0.009 0.001 TYR R 369 ARG 0.003 0.001 ARG R 253 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.269 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 0.1895 time to fit residues: 10.9379 Evaluate side-chains 51 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.223304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.207385 restraints weight = 5425.590| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.21 r_work: 0.4085 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4089 r_free = 0.4089 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4089 r_free = 0.4089 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2554 Z= 0.198 Angle : 0.619 8.731 3474 Z= 0.315 Chirality : 0.042 0.272 418 Planarity : 0.005 0.038 416 Dihedral : 4.505 21.593 337 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.77 % Allowed : 12.06 % Favored : 86.17 % 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: 2.00 (0.48), residues: 307 helix: 1.94 (0.32), residues: 244 sheet: -0.52 (1.37), residues: 10 loop : -1.19 (0.95), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 PHE 0.031 0.002 PHE R 100 TYR 0.017 0.001 TYR R 387 ARG 0.003 0.001 ARG R 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.265 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 0.1960 time to fit residues: 11.7641 Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.224791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.208978 restraints weight = 5440.194| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.22 r_work: 0.4092 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2554 Z= 0.167 Angle : 0.589 7.260 3474 Z= 0.301 Chirality : 0.041 0.277 418 Planarity : 0.004 0.038 416 Dihedral : 4.383 21.807 337 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.84 % Allowed : 10.64 % Favored : 86.52 % 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: 2.21 (0.49), residues: 307 helix: 2.07 (0.32), residues: 244 sheet: -0.35 (1.36), residues: 10 loop : -1.09 (0.98), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 276 HIS 0.003 0.001 HIS R 258 PHE 0.034 0.002 PHE R 100 TYR 0.009 0.001 TYR R 350 ARG 0.003 0.001 ARG R 253 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.263 Fit side-chains REVERT: R 134 ASN cc_start: 0.7478 (OUTLIER) cc_final: 0.7270 (p0) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.1813 time to fit residues: 10.5396 Evaluate side-chains 53 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 25 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.219730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.203595 restraints weight = 5432.661| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 2.22 r_work: 0.4064 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4041 r_free = 0.4041 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4041 r_free = 0.4041 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2554 Z= 0.305 Angle : 0.730 9.130 3474 Z= 0.371 Chirality : 0.046 0.312 418 Planarity : 0.005 0.038 416 Dihedral : 4.727 23.360 337 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.48 % Allowed : 11.70 % Favored : 85.82 % 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: 1.45 (0.47), residues: 307 helix: 1.56 (0.31), residues: 244 sheet: -0.63 (1.27), residues: 10 loop : -1.45 (0.92), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 276 HIS 0.007 0.002 HIS R 258 PHE 0.026 0.003 PHE R 100 TYR 0.011 0.002 TYR R 369 ARG 0.007 0.001 ARG R 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.277 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.1750 time to fit residues: 10.4090 Evaluate side-chains 55 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.222691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.205803 restraints weight = 6699.758| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.57 r_work: 0.4048 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2554 Z= 0.205 Angle : 0.647 8.531 3474 Z= 0.329 Chirality : 0.043 0.285 418 Planarity : 0.004 0.034 416 Dihedral : 4.642 23.449 337 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.13 % Allowed : 12.41 % Favored : 85.46 % 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: 307 helix: 1.78 (0.32), residues: 244 sheet: -0.43 (1.28), residues: 10 loop : -1.38 (0.94), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 276 HIS 0.005 0.001 HIS R 258 PHE 0.033 0.002 PHE R 100 TYR 0.010 0.001 TYR R 350 ARG 0.003 0.000 ARG R 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.263 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 47 average time/residue: 0.1917 time to fit residues: 10.4295 Evaluate side-chains 49 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 18 optimal weight: 7.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.223779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.205097 restraints weight = 8831.412| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 3.25 r_work: 0.4024 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2554 Z= 0.187 Angle : 0.622 8.415 3474 Z= 0.317 Chirality : 0.042 0.285 418 Planarity : 0.004 0.029 416 Dihedral : 4.518 22.662 337 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.48 % Allowed : 12.41 % Favored : 85.11 % 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: 1.99 (0.48), residues: 307 helix: 1.96 (0.32), residues: 244 sheet: -0.30 (1.31), residues: 10 loop : -1.37 (0.94), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 21 HIS 0.004 0.001 HIS R 258 PHE 0.033 0.002 PHE R 100 TYR 0.010 0.001 TYR R 350 ARG 0.003 0.001 ARG R 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.257 Fit side-chains REVERT: R 134 ASN cc_start: 0.7495 (OUTLIER) cc_final: 0.7272 (p0) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.1830 time to fit residues: 10.2928 Evaluate side-chains 51 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.223480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.210113 restraints weight = 3316.563| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 1.53 r_work: 0.4122 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4030 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4037 r_free = 0.4037 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4037 r_free = 0.4037 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.187 2554 Z= 0.486 Angle : 1.461 59.193 3474 Z= 0.885 Chirality : 0.052 0.637 418 Planarity : 0.005 0.030 416 Dihedral : 4.550 22.593 337 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.48 % Allowed : 12.41 % Favored : 85.11 % Cbeta Deviations : 0.33 % 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: 2.02 (0.48), residues: 307 helix: 1.97 (0.32), residues: 244 sheet: -0.30 (1.31), residues: 10 loop : -1.35 (0.94), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 PHE 0.031 0.002 PHE R 100 TYR 0.009 0.001 TYR R 350 ARG 0.001 0.000 ARG R 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.271 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 47 average time/residue: 0.1874 time to fit residues: 10.3042 Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 365 LEU Chi-restraints excluded: chain R residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.223697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.207600 restraints weight = 5468.149| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.29 r_work: 0.4073 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4074 r_free = 0.4074 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4074 r_free = 0.4074 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.187 2554 Z= 0.486 Angle : 1.461 59.200 3474 Z= 0.885 Chirality : 0.052 0.636 418 Planarity : 0.005 0.030 416 Dihedral : 4.550 22.592 337 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.13 % Allowed : 12.41 % Favored : 85.46 % Cbeta Deviations : 0.33 % 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: 2.02 (0.48), residues: 307 helix: 1.97 (0.32), residues: 244 sheet: -0.30 (1.31), residues: 10 loop : -1.35 (0.94), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 276 HIS 0.004 0.001 HIS R 258 PHE 0.031 0.002 PHE R 100 TYR 0.009 0.001 TYR R 350 ARG 0.001 0.000 ARG R 199 =============================================================================== Job complete usr+sys time: 1529.76 seconds wall clock time: 27 minutes 53.34 seconds (1673.34 seconds total)