Starting phenix.real_space_refine on Tue Feb 11 05:55:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ul2_26589/02_2025/7ul2_26589.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ul2_26589/02_2025/7ul2_26589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ul2_26589/02_2025/7ul2_26589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ul2_26589/02_2025/7ul2_26589.map" model { file = "/net/cci-nas-00/data/ceres_data/7ul2_26589/02_2025/7ul2_26589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ul2_26589/02_2025/7ul2_26589.cif" } resolution = 2.4 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= -0.001 sd= 0.088 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 1879 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: 6 Type Number sf(0) Gaussians S 15 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 1724 2.51 5 N 428 2.21 5 O 455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2624 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2185 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 277} Chain breaks: 3 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 383 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 59} Chain breaks: 4 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 56 Unusual residues: {' NA': 1, 'Q6Q': 1} Classifications: {'undetermined': 2, 'water': 13} Link IDs: {None: 14} Time building chain proxies: 2.78, per 1000 atoms: 1.06 Number of scatterers: 2624 At special positions: 0 Unit cell: (69.416, 50.3266, 103.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 15 16.00 Na 1 11.00 O 455 8.00 N 428 7.00 C 1724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.05 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: 0.71 Conformation dependent library (CDL) restraints added in 293.6 milliseconds 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 2 sheets defined 73.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'R' and resid 60 through 90 removed outlier: 3.575A pdb=" N PHE R 86 " --> pdb=" O THR R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 118 removed outlier: 3.919A pdb=" N HIS R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 127 removed outlier: 3.775A pdb=" N VAL R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 172 removed outlier: 3.598A pdb=" N GLY R 140 " --> pdb=" O PHE R 136 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR R 145 " --> pdb=" O CYS R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 180 removed outlier: 3.784A pdb=" N LYS R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR R 178 " --> pdb=" O PHE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 200 Processing helix chain 'R' and resid 200 through 206 removed outlier: 4.015A pdb=" N LEU R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 245 Processing helix chain 'R' and resid 245 through 264 Processing helix chain 'R' and resid 272 through 329 Proline residue: R 318 - end of helix removed outlier: 3.545A pdb=" N PHE R 326 " --> pdb=" O ARG R 322 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS R 327 " --> pdb=" O ARG R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 368 removed outlier: 3.505A pdb=" N PHE R 353 " --> pdb=" O THR R 349 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR R 354 " --> pdb=" O ASN R 350 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR R 358 " --> pdb=" O TYR R 354 " (cutoff:3.500A) removed outlier: 4.698A 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 379 removed outlier: 3.512A pdb=" N ARG R 372 " --> pdb=" O SER R 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 207 through 212 Processing sheet with id=AA2, first strand: chain 'D' and resid 59 through 60 removed outlier: 6.067A pdb=" N GLU D 100 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET D 36 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN D 98 " --> pdb=" O MET D 36 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 597 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: 0.67 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 605 1.33 - 1.47: 939 1.47 - 1.60: 1106 1.60 - 1.74: 1 1.74 - 1.88: 24 Bond restraints: 2675 Sorted by residual: bond pdb=" C2 Q6Q R 501 " pdb=" O1 Q6Q R 501 " ideal model delta sigma weight residual 1.246 1.196 0.050 2.00e-02 2.50e+03 6.36e+00 bond pdb=" C2 Q6Q R 501 " pdb=" O2 Q6Q R 501 " ideal model delta sigma weight residual 1.244 1.194 0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 Q6Q R 501 " pdb=" C2 Q6Q R 501 " ideal model delta sigma weight residual 1.573 1.524 0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" CB CYS R 224 " pdb=" SG CYS R 224 " ideal model delta sigma weight residual 1.808 1.878 -0.070 3.30e-02 9.18e+02 4.44e+00 bond pdb=" CB ARG R 303 " pdb=" CG ARG R 303 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.09e+00 ... (remaining 2670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 3504 2.17 - 4.34: 133 4.34 - 6.51: 25 6.51 - 8.68: 2 8.68 - 10.85: 1 Bond angle restraints: 3665 Sorted by residual: angle pdb=" N ILE R 359 " pdb=" CA ILE R 359 " pdb=" C ILE R 359 " ideal model delta sigma weight residual 110.72 114.28 -3.56 1.01e+00 9.80e-01 1.24e+01 angle pdb=" N ASN R 360 " pdb=" CA ASN R 360 " pdb=" C ASN R 360 " ideal model delta sigma weight residual 109.81 117.53 -7.72 2.21e+00 2.05e-01 1.22e+01 angle pdb=" CA LEU R 258 " pdb=" CB LEU R 258 " pdb=" CG LEU R 258 " ideal model delta sigma weight residual 116.30 105.45 10.85 3.50e+00 8.16e-02 9.61e+00 angle pdb=" N TYR R 328 " pdb=" CA TYR R 328 " pdb=" C TYR R 328 " ideal model delta sigma weight residual 113.30 117.38 -4.08 1.34e+00 5.57e-01 9.28e+00 angle pdb=" CA TYR R 256 " pdb=" CB TYR R 256 " pdb=" CG TYR R 256 " ideal model delta sigma weight residual 113.90 108.43 5.47 1.80e+00 3.09e-01 9.25e+00 ... (remaining 3660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 1460 17.86 - 35.72: 60 35.72 - 53.58: 22 53.58 - 71.45: 3 71.45 - 89.31: 2 Dihedral angle restraints: 1547 sinusoidal: 530 harmonic: 1017 Sorted by residual: dihedral pdb=" N ASN R 126 " pdb=" CA ASN R 126 " pdb=" CB ASN R 126 " pdb=" CG ASN R 126 " ideal model delta sinusoidal sigma weight residual -180.00 -120.54 -59.46 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG R 323 " pdb=" CB ARG R 323 " pdb=" CG ARG R 323 " pdb=" CD ARG R 323 " ideal model delta sinusoidal sigma weight residual -60.00 -113.69 53.69 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CA ARG D 32 " pdb=" CB ARG D 32 " pdb=" CG ARG D 32 " pdb=" CD ARG D 32 " ideal model delta sinusoidal sigma weight residual -60.00 -111.39 51.39 3 1.50e+01 4.44e-03 9.01e+00 ... (remaining 1544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 280 0.052 - 0.103: 125 0.103 - 0.155: 28 0.155 - 0.207: 9 0.207 - 0.258: 1 Chirality restraints: 443 Sorted by residual: chirality pdb=" CA ASN R 360 " pdb=" N ASN R 360 " pdb=" C ASN R 360 " pdb=" CB ASN R 360 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA TYR R 145 " pdb=" N TYR R 145 " pdb=" C TYR R 145 " pdb=" CB TYR R 145 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CA PHE R 127 " pdb=" N PHE R 127 " pdb=" C PHE R 127 " pdb=" CB PHE R 127 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 440 not shown) Planarity restraints: 440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C Q6Q R 501 " -0.015 2.00e-02 2.50e+03 2.26e-02 1.03e+01 pdb=" C12 Q6Q R 501 " 0.036 2.00e-02 2.50e+03 pdb=" C13 Q6Q R 501 " 0.006 2.00e-02 2.50e+03 pdb=" C14 Q6Q R 501 " -0.011 2.00e-02 2.50e+03 pdb=" C22 Q6Q R 501 " 0.009 2.00e-02 2.50e+03 pdb=" C23 Q6Q R 501 " 0.027 2.00e-02 2.50e+03 pdb=" N1 Q6Q R 501 " -0.014 2.00e-02 2.50e+03 pdb=" N2 Q6Q R 501 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 Q6Q R 501 " -0.046 2.00e-02 2.50e+03 1.77e-02 9.37e+00 pdb=" C24 Q6Q R 501 " 0.003 2.00e-02 2.50e+03 pdb=" C25 Q6Q R 501 " -0.010 2.00e-02 2.50e+03 pdb=" C26 Q6Q R 501 " -0.005 2.00e-02 2.50e+03 pdb=" C27 Q6Q R 501 " 0.008 2.00e-02 2.50e+03 pdb=" C28 Q6Q R 501 " 0.001 2.00e-02 2.50e+03 pdb=" C29 Q6Q R 501 " 0.001 2.00e-02 2.50e+03 pdb=" C30 Q6Q R 501 " 0.008 2.00e-02 2.50e+03 pdb=" C31 Q6Q R 501 " -0.001 2.00e-02 2.50e+03 pdb=" N2 Q6Q R 501 " 0.037 2.00e-02 2.50e+03 pdb=" N3 Q6Q R 501 " 0.000 2.00e-02 2.50e+03 pdb="CL Q6Q R 501 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 334 " 0.019 2.00e-02 2.50e+03 1.28e-02 4.11e+00 pdb=" CG TRP R 334 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP R 334 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 334 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 334 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 334 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP R 334 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 334 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 334 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 334 " 0.004 2.00e-02 2.50e+03 ... (remaining 437 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 743 2.82 - 3.34: 2497 3.34 - 3.86: 4251 3.86 - 4.38: 4846 4.38 - 4.90: 8051 Nonbonded interactions: 20388 Sorted by model distance: nonbonded pdb=" N TYR D 39 " pdb=" O TYR D 96 " model vdw 2.306 3.120 nonbonded pdb=" O TYR D 39 " pdb=" N TYR D 96 " model vdw 2.371 3.120 nonbonded pdb=" O PHE R 74 " pdb=" OG1 THR R 78 " model vdw 2.379 3.040 nonbonded pdb=" OD1 ASP R 112 " pdb="NA NA R 502 " model vdw 2.385 2.470 nonbonded pdb=" O LYS R 63 " pdb=" OG1 THR R 67 " model vdw 2.428 3.040 ... (remaining 20383 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=0.00 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: 1.430 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.780 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:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 0.070 2675 Z= 0.499 Angle : 1.016 10.850 3665 Z= 0.560 Chirality : 0.061 0.258 443 Planarity : 0.006 0.040 440 Dihedral : 12.544 89.306 884 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.84 % Allowed : 7.56 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.60 (0.41), residues: 329 helix: 1.95 (0.30), residues: 224 sheet: 1.57 (1.66), residues: 9 loop : -1.17 (0.52), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP R 334 HIS 0.004 0.002 HIS R 172 PHE 0.026 0.004 PHE R 337 TYR 0.031 0.004 TYR R 256 ARG 0.012 0.002 ARG R 299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.290 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 1.1311 time to fit residues: 58.0756 Evaluate side-chains 40 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 126 ASN Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.149765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129493 restraints weight = 2978.155| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.38 r_work: 0.3396 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2675 Z= 0.196 Angle : 0.574 8.946 3665 Z= 0.323 Chirality : 0.041 0.175 443 Planarity : 0.004 0.028 440 Dihedral : 5.769 50.044 430 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.10 % Allowed : 7.56 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.96 (0.44), residues: 329 helix: 3.25 (0.31), residues: 228 sheet: 1.56 (1.72), residues: 9 loop : -1.61 (0.50), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 316 HIS 0.002 0.001 HIS R 229 PHE 0.016 0.002 PHE R 375 TYR 0.015 0.002 TYR R 256 ARG 0.002 0.000 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.264 Fit side-chains REVERT: R 65 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7291 (tt) outliers start: 5 outliers final: 2 residues processed: 42 average time/residue: 1.0408 time to fit residues: 45.1206 Evaluate side-chains 39 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 0.0370 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126921 restraints weight = 2940.412| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.38 r_work: 0.3369 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2675 Z= 0.197 Angle : 0.546 8.178 3665 Z= 0.307 Chirality : 0.040 0.149 443 Planarity : 0.004 0.032 440 Dihedral : 4.980 44.362 428 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 3.36 % Allowed : 6.72 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 3.04 (0.44), residues: 329 helix: 3.30 (0.31), residues: 229 sheet: 1.45 (1.99), residues: 9 loop : -1.58 (0.51), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 PHE 0.015 0.002 PHE R 375 TYR 0.015 0.002 TYR R 256 ARG 0.002 0.000 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.228 Fit side-chains REVERT: R 65 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7214 (tt) REVERT: R 123 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7829 (tt0) outliers start: 8 outliers final: 2 residues processed: 41 average time/residue: 1.0298 time to fit residues: 43.5574 Evaluate side-chains 40 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 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 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.143509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122796 restraints weight = 2904.931| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.37 r_work: 0.3314 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2675 Z= 0.284 Angle : 0.635 8.519 3665 Z= 0.353 Chirality : 0.043 0.154 443 Planarity : 0.005 0.039 440 Dihedral : 5.169 45.909 428 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.36 % Allowed : 7.98 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.48 (0.44), residues: 329 helix: 2.82 (0.31), residues: 235 sheet: 1.00 (1.75), residues: 9 loop : -1.91 (0.51), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 316 HIS 0.003 0.001 HIS R 229 PHE 0.018 0.002 PHE R 375 TYR 0.018 0.002 TYR R 256 ARG 0.002 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.274 Fit side-chains REVERT: R 65 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7340 (tt) REVERT: R 123 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7873 (tt0) outliers start: 8 outliers final: 4 residues processed: 40 average time/residue: 1.0158 time to fit residues: 41.9457 Evaluate side-chains 43 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 322 ARG Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 340 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.148740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128229 restraints weight = 2929.590| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.37 r_work: 0.3388 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2675 Z= 0.168 Angle : 0.512 8.230 3665 Z= 0.287 Chirality : 0.038 0.150 443 Planarity : 0.004 0.041 440 Dihedral : 4.948 43.264 428 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.52 % Allowed : 10.50 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.89 (0.44), residues: 329 helix: 3.25 (0.31), residues: 229 sheet: 0.72 (1.72), residues: 9 loop : -1.76 (0.51), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 PHE 0.014 0.002 PHE R 375 TYR 0.013 0.001 TYR R 256 ARG 0.001 0.000 ARG R 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.263 Fit side-chains REVERT: R 65 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7107 (mt) REVERT: R 123 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7821 (tt0) outliers start: 6 outliers final: 2 residues processed: 38 average time/residue: 1.0602 time to fit residues: 41.5098 Evaluate side-chains 39 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 2 optimal weight: 0.0670 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.131509 restraints weight = 2972.438| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.39 r_work: 0.3429 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2675 Z= 0.146 Angle : 0.473 7.941 3665 Z= 0.265 Chirality : 0.037 0.143 443 Planarity : 0.004 0.040 440 Dihedral : 4.767 42.547 428 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.10 % Allowed : 11.34 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 3.14 (0.45), residues: 329 helix: 3.35 (0.32), residues: 235 sheet: 0.81 (1.86), residues: 9 loop : -1.75 (0.53), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 129 HIS 0.004 0.001 HIS R 343 PHE 0.013 0.001 PHE R 375 TYR 0.012 0.001 TYR R 144 ARG 0.001 0.000 ARG R 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.275 Fit side-chains REVERT: R 123 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7844 (tt0) outliers start: 5 outliers final: 2 residues processed: 39 average time/residue: 1.0492 time to fit residues: 42.2774 Evaluate side-chains 36 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 19 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127703 restraints weight = 3034.936| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.43 r_work: 0.3374 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2675 Z= 0.182 Angle : 0.522 8.047 3665 Z= 0.290 Chirality : 0.038 0.144 443 Planarity : 0.004 0.044 440 Dihedral : 4.846 43.686 428 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.52 % Allowed : 11.76 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 3.00 (0.45), residues: 329 helix: 3.25 (0.32), residues: 235 sheet: 0.51 (1.76), residues: 9 loop : -1.78 (0.54), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 316 HIS 0.004 0.001 HIS R 343 PHE 0.014 0.002 PHE R 375 TYR 0.014 0.001 TYR R 256 ARG 0.001 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.326 Fit side-chains REVERT: R 65 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7122 (mt) REVERT: R 123 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7877 (tt0) outliers start: 6 outliers final: 3 residues processed: 38 average time/residue: 1.0752 time to fit residues: 42.1199 Evaluate side-chains 39 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 22 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.0170 chunk 0 optimal weight: 2.9990 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.153275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132452 restraints weight = 2961.243| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.43 r_work: 0.3439 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2675 Z= 0.140 Angle : 0.466 7.853 3665 Z= 0.261 Chirality : 0.037 0.138 443 Planarity : 0.004 0.044 440 Dihedral : 4.738 42.413 428 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.52 % Allowed : 11.34 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 3.24 (0.46), residues: 329 helix: 3.43 (0.32), residues: 235 sheet: 0.46 (1.77), residues: 9 loop : -1.69 (0.55), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 129 HIS 0.004 0.001 HIS R 343 PHE 0.012 0.001 PHE R 375 TYR 0.012 0.001 TYR R 144 ARG 0.001 0.000 ARG R 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.265 Fit side-chains REVERT: R 65 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7026 (mt) REVERT: R 123 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7868 (tt0) outliers start: 6 outliers final: 3 residues processed: 37 average time/residue: 1.1176 time to fit residues: 42.6137 Evaluate side-chains 39 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.147671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126827 restraints weight = 2928.650| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.38 r_work: 0.3367 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2675 Z= 0.194 Angle : 0.536 8.129 3665 Z= 0.298 Chirality : 0.039 0.146 443 Planarity : 0.004 0.043 440 Dihedral : 4.862 44.060 428 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.94 % Allowed : 11.76 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.93 (0.45), residues: 329 helix: 3.21 (0.32), residues: 235 sheet: 0.00 (1.64), residues: 9 loop : -1.80 (0.55), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 316 HIS 0.004 0.001 HIS R 343 PHE 0.014 0.002 PHE R 375 TYR 0.014 0.002 TYR R 256 ARG 0.001 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.266 Fit side-chains REVERT: R 65 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7138 (mt) REVERT: R 123 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7858 (tt0) outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 1.0521 time to fit residues: 42.3373 Evaluate side-chains 40 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.148309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127470 restraints weight = 2960.678| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.39 r_work: 0.3373 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2675 Z= 0.187 Angle : 0.528 8.117 3665 Z= 0.294 Chirality : 0.039 0.145 443 Planarity : 0.004 0.044 440 Dihedral : 4.882 43.845 428 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.94 % Allowed : 11.76 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.88 (0.45), residues: 329 helix: 3.20 (0.32), residues: 235 sheet: -0.10 (1.58), residues: 9 loop : -1.89 (0.55), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 316 HIS 0.004 0.001 HIS R 343 PHE 0.013 0.002 PHE R 375 TYR 0.014 0.002 TYR R 256 ARG 0.001 0.000 ARG D 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.329 Fit side-chains REVERT: R 65 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7140 (mt) REVERT: R 123 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7846 (tt0) outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 1.0513 time to fit residues: 42.3396 Evaluate side-chains 40 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.146294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.125462 restraints weight = 2921.775| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.38 r_work: 0.3346 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2675 Z= 0.219 Angle : 0.565 8.295 3665 Z= 0.313 Chirality : 0.040 0.149 443 Planarity : 0.005 0.045 440 Dihedral : 4.958 44.718 428 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.94 % Allowed : 12.18 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.68 (0.45), residues: 329 helix: 3.05 (0.32), residues: 235 sheet: -0.32 (1.50), residues: 9 loop : -1.93 (0.54), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 316 HIS 0.004 0.001 HIS R 343 PHE 0.013 0.002 PHE R 375 TYR 0.016 0.002 TYR R 256 ARG 0.001 0.000 ARG D 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2345.79 seconds wall clock time: 42 minutes 6.81 seconds (2526.81 seconds total)