Starting phenix.real_space_refine on Wed Jul 23 09:32:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsn_38623/07_2025/8xsn_38623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsn_38623/07_2025/8xsn_38623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xsn_38623/07_2025/8xsn_38623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsn_38623/07_2025/8xsn_38623.map" model { file = "/net/cci-nas-00/data/ceres_data/8xsn_38623/07_2025/8xsn_38623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsn_38623/07_2025/8xsn_38623.cif" } resolution = 3.29 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= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 1807 2.51 5 N 417 2.21 5 O 453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 2703 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2676 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'RBF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.87, per 1000 atoms: 1.06 Number of scatterers: 2703 At special positions: 0 Unit cell: (60.35, 71.4, 73.95, 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 26 16.00 O 453 8.00 N 417 7.00 C 1807 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 324.5 milliseconds 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 662 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 85.2% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 removed outlier: 4.032A pdb=" N MET A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 31 Proline residue: A 28 - end of helix Processing helix chain 'A' and resid 36 through 38 No H-bonds generated for 'chain 'A' and resid 36 through 38' Processing helix chain 'A' and resid 39 through 51 removed outlier: 3.618A pdb=" N TYR A 43 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 65 removed outlier: 3.807A pdb=" N LEU A 56 " --> pdb=" O ASN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 93 removed outlier: 3.654A pdb=" N ILE A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A 91 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 126 removed outlier: 3.979A pdb=" N VAL A 124 " --> pdb=" O CYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.885A pdb=" N MET A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 126 through 131' Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 137 through 147 removed outlier: 4.057A pdb=" N PHE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 160 removed outlier: 3.917A pdb=" N ALA A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 242 removed outlier: 3.747A pdb=" N PHE A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLN A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 316 removed outlier: 4.132A pdb=" N ALA A 301 " --> pdb=" O PRO A 297 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 303 " --> pdb=" O HIS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 320 Processing helix chain 'A' and resid 321 through 327 Processing helix chain 'A' and resid 330 through 355 removed outlier: 3.805A pdb=" N TYR A 334 " --> pdb=" O GLY A 330 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Proline residue: A 346 - end of helix Processing helix chain 'A' and resid 359 through 382 removed outlier: 3.565A pdb=" N MET A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 425 removed outlier: 3.694A pdb=" N GLU A 396 " --> pdb=" O HIS A 392 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 397 " --> pdb=" O TRP A 393 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 413 " --> pdb=" O CYS A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 452 Proline residue: A 449 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.513A pdb=" N SER A 97 " --> pdb=" O HIS A 104 " (cutoff:3.500A) 195 hydrogen bonds defined for protein. 582 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: 0.73 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 394 1.30 - 1.43: 771 1.43 - 1.56: 1573 1.56 - 1.68: 0 1.68 - 1.81: 40 Bond restraints: 2778 Sorted by residual: bond pdb=" C4 RBF A 501 " pdb=" C4A RBF A 501 " ideal model delta sigma weight residual 1.481 1.346 0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" C10 RBF A 501 " pdb=" C4A RBF A 501 " ideal model delta sigma weight residual 1.440 1.350 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C9A RBF A 501 " pdb=" N10 RBF A 501 " ideal model delta sigma weight residual 1.376 1.326 0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C2 RBF A 501 " pdb=" N3 RBF A 501 " ideal model delta sigma weight residual 1.397 1.348 0.049 2.00e-02 2.50e+03 5.92e+00 bond pdb=" C4 RBF A 501 " pdb=" N3 RBF A 501 " ideal model delta sigma weight residual 1.362 1.314 0.048 2.00e-02 2.50e+03 5.68e+00 ... (remaining 2773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 3782 3.78 - 7.56: 25 7.56 - 11.33: 1 11.33 - 15.11: 0 15.11 - 18.89: 1 Bond angle restraints: 3809 Sorted by residual: angle pdb=" N GLY A 160 " pdb=" CA GLY A 160 " pdb=" C GLY A 160 " ideal model delta sigma weight residual 115.08 133.97 -18.89 1.54e+00 4.22e-01 1.50e+02 angle pdb=" N SER A 161 " pdb=" CA SER A 161 " pdb=" C SER A 161 " ideal model delta sigma weight residual 111.00 120.43 -9.43 2.80e+00 1.28e-01 1.13e+01 angle pdb=" C SER A 384 " pdb=" N PRO A 385 " pdb=" CA PRO A 385 " ideal model delta sigma weight residual 127.00 133.83 -6.83 2.40e+00 1.74e-01 8.10e+00 angle pdb=" C CYS A 409 " pdb=" N LEU A 410 " pdb=" CA LEU A 410 " ideal model delta sigma weight residual 121.52 116.39 5.13 1.84e+00 2.95e-01 7.78e+00 angle pdb=" N SER A 161 " pdb=" CA SER A 161 " pdb=" CB SER A 161 " ideal model delta sigma weight residual 110.50 115.18 -4.68 1.70e+00 3.46e-01 7.56e+00 ... (remaining 3804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 1404 16.45 - 32.90: 143 32.90 - 49.35: 32 49.35 - 65.80: 4 65.80 - 82.25: 2 Dihedral angle restraints: 1585 sinusoidal: 561 harmonic: 1024 Sorted by residual: dihedral pdb=" N SER A 161 " pdb=" C SER A 161 " pdb=" CA SER A 161 " pdb=" CB SER A 161 " ideal model delta harmonic sigma weight residual 122.80 137.32 -14.52 0 2.50e+00 1.60e-01 3.37e+01 dihedral pdb=" C SER A 161 " pdb=" N SER A 161 " pdb=" CA SER A 161 " pdb=" CB SER A 161 " ideal model delta harmonic sigma weight residual -122.60 -135.17 12.57 0 2.50e+00 1.60e-01 2.53e+01 dihedral pdb=" CA VAL A 451 " pdb=" C VAL A 451 " pdb=" N ASN A 452 " pdb=" CA ASN A 452 " ideal model delta harmonic sigma weight residual -180.00 -162.77 -17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 1582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 467 0.130 - 0.259: 4 0.259 - 0.388: 0 0.388 - 0.518: 0 0.518 - 0.647: 1 Chirality restraints: 472 Sorted by residual: chirality pdb=" CA SER A 161 " pdb=" N SER A 161 " pdb=" C SER A 161 " pdb=" CB SER A 161 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA MET A 32 " pdb=" N MET A 32 " pdb=" C MET A 32 " pdb=" CB MET A 32 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C4' RBF A 501 " pdb=" C3' RBF A 501 " pdb=" C5' RBF A 501 " pdb=" O4' RBF A 501 " both_signs ideal model delta sigma weight residual False -2.27 -2.49 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 469 not shown) Planarity restraints: 452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 27 " 0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO A 28 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 28 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 28 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 318 " -0.034 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO A 319 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 319 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 319 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 355 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 356 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 356 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 356 " 0.017 5.00e-02 4.00e+02 ... (remaining 449 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 626 2.77 - 3.30: 2656 3.30 - 3.84: 4252 3.84 - 4.37: 4962 4.37 - 4.90: 8690 Nonbonded interactions: 21186 Sorted by model distance: nonbonded pdb=" O LEU A 225 " pdb=" OG SER A 228 " model vdw 2.241 3.040 nonbonded pdb=" NH2 ARG A 422 " pdb=" OD1 ASP A 423 " model vdw 2.243 3.120 nonbonded pdb=" O PRO A 346 " pdb=" OG SER A 349 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASN A 357 " pdb=" OG SER A 359 " model vdw 2.263 3.040 nonbonded pdb=" O ARG A 422 " pdb=" NH2 ARG A 426 " model vdw 2.289 3.120 ... (remaining 21181 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.100 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.007 0.135 2778 Z= 0.313 Angle : 0.845 18.888 3809 Z= 0.442 Chirality : 0.054 0.647 472 Planarity : 0.006 0.060 452 Dihedral : 14.246 82.253 923 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.68 % Allowed : 10.27 % Favored : 89.04 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 5.56 % 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: -1.43 (0.40), residues: 351 helix: -0.62 (0.29), residues: 261 sheet: None (None), residues: 0 loop : -1.48 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 93 HIS 0.005 0.001 HIS A 335 PHE 0.015 0.002 PHE A 218 TYR 0.010 0.001 TYR A 412 ARG 0.003 0.001 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.13404 ( 195) hydrogen bonds : angle 5.54532 ( 582) covalent geometry : bond 0.00710 ( 2778) covalent geometry : angle 0.84503 ( 3809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.282 Fit side-chains REVERT: A 87 ILE cc_start: 0.6226 (mt) cc_final: 0.5874 (mt) REVERT: A 98 TRP cc_start: 0.8193 (t-100) cc_final: 0.7796 (t-100) REVERT: A 219 SER cc_start: 0.7860 (p) cc_final: 0.7625 (t) outliers start: 2 outliers final: 1 residues processed: 49 average time/residue: 0.0891 time to fit residues: 5.8791 Evaluate side-chains 39 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS A 159 GLN A 392 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.154482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.133108 restraints weight = 3676.130| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.96 r_work: 0.3374 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2778 Z= 0.133 Angle : 0.559 5.584 3809 Z= 0.278 Chirality : 0.037 0.109 472 Planarity : 0.005 0.047 452 Dihedral : 6.241 38.038 384 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.05 % Allowed : 15.07 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.51 (0.42), residues: 351 helix: 0.81 (0.30), residues: 265 sheet: None (None), residues: 0 loop : -0.96 (0.63), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 24 HIS 0.002 0.001 HIS A 335 PHE 0.011 0.001 PHE A 406 TYR 0.006 0.001 TYR A 324 ARG 0.001 0.000 ARG A 422 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 195) hydrogen bonds : angle 3.91289 ( 582) covalent geometry : bond 0.00301 ( 2778) covalent geometry : angle 0.55919 ( 3809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.285 Fit side-chains REVERT: A 60 LEU cc_start: 0.8505 (mt) cc_final: 0.8292 (mp) REVERT: A 358 ARG cc_start: 0.7690 (mtp180) cc_final: 0.7226 (mpt180) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.1050 time to fit residues: 6.8443 Evaluate side-chains 43 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 419 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.0170 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.152085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130275 restraints weight = 3676.252| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.02 r_work: 0.3361 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2778 Z= 0.150 Angle : 0.571 5.679 3809 Z= 0.282 Chirality : 0.038 0.111 472 Planarity : 0.006 0.062 452 Dihedral : 6.233 39.588 384 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.71 % Allowed : 17.12 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.13 (0.43), residues: 351 helix: 1.30 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -0.90 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 98 HIS 0.004 0.001 HIS A 335 PHE 0.013 0.001 PHE A 406 TYR 0.008 0.001 TYR A 412 ARG 0.001 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 195) hydrogen bonds : angle 3.81598 ( 582) covalent geometry : bond 0.00352 ( 2778) covalent geometry : angle 0.57056 ( 3809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.269 Fit side-chains REVERT: A 358 ARG cc_start: 0.7685 (mtp-110) cc_final: 0.7221 (mpt180) REVERT: A 412 TYR cc_start: 0.8062 (t80) cc_final: 0.7711 (t80) outliers start: 5 outliers final: 5 residues processed: 48 average time/residue: 0.1015 time to fit residues: 6.3980 Evaluate side-chains 44 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 419 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.152990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.131261 restraints weight = 3731.261| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.02 r_work: 0.3365 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2778 Z= 0.143 Angle : 0.565 6.557 3809 Z= 0.276 Chirality : 0.038 0.112 472 Planarity : 0.005 0.046 452 Dihedral : 6.181 39.685 384 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.42 % Allowed : 18.49 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.54 (0.43), residues: 351 helix: 1.56 (0.31), residues: 269 sheet: None (None), residues: 0 loop : -0.68 (0.64), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 98 HIS 0.003 0.001 HIS A 335 PHE 0.013 0.001 PHE A 406 TYR 0.008 0.001 TYR A 412 ARG 0.001 0.000 ARG A 426 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 195) hydrogen bonds : angle 3.74993 ( 582) covalent geometry : bond 0.00339 ( 2778) covalent geometry : angle 0.56482 ( 3809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.316 Fit side-chains REVERT: A 358 ARG cc_start: 0.7707 (mtp-110) cc_final: 0.7225 (mpt180) REVERT: A 412 TYR cc_start: 0.8073 (t80) cc_final: 0.7737 (t80) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 0.1102 time to fit residues: 6.7385 Evaluate side-chains 47 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 419 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 0.0470 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.157173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.135661 restraints weight = 3771.300| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.98 r_work: 0.3409 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2778 Z= 0.117 Angle : 0.520 6.378 3809 Z= 0.253 Chirality : 0.036 0.107 472 Planarity : 0.005 0.040 452 Dihedral : 6.060 42.829 384 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.08 % Allowed : 18.49 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.11 (0.44), residues: 351 helix: 1.85 (0.31), residues: 273 sheet: None (None), residues: 0 loop : -0.10 (0.68), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 98 HIS 0.002 0.001 HIS A 335 PHE 0.012 0.001 PHE A 406 TYR 0.007 0.001 TYR A 412 ARG 0.001 0.000 ARG A 426 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 195) hydrogen bonds : angle 3.53365 ( 582) covalent geometry : bond 0.00261 ( 2778) covalent geometry : angle 0.52027 ( 3809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.292 Fit side-chains REVERT: A 358 ARG cc_start: 0.7644 (mtp-110) cc_final: 0.7186 (mtt90) REVERT: A 412 TYR cc_start: 0.7971 (t80) cc_final: 0.7664 (t80) REVERT: A 424 LEU cc_start: 0.5691 (OUTLIER) cc_final: 0.5337 (mt) REVERT: A 447 MET cc_start: 0.8459 (mmm) cc_final: 0.8172 (tpt) outliers start: 9 outliers final: 4 residues processed: 47 average time/residue: 0.1064 time to fit residues: 6.5370 Evaluate side-chains 45 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN A 315 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.153311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.131862 restraints weight = 3776.110| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.01 r_work: 0.3373 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2778 Z= 0.143 Angle : 0.562 6.350 3809 Z= 0.272 Chirality : 0.038 0.111 472 Planarity : 0.005 0.041 452 Dihedral : 6.087 40.684 384 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.11 % Allowed : 18.49 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.09 (0.44), residues: 351 helix: 1.81 (0.30), residues: 273 sheet: None (None), residues: 0 loop : -0.01 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 98 HIS 0.003 0.001 HIS A 335 PHE 0.013 0.001 PHE A 406 TYR 0.008 0.001 TYR A 412 ARG 0.001 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 195) hydrogen bonds : angle 3.68573 ( 582) covalent geometry : bond 0.00339 ( 2778) covalent geometry : angle 0.56214 ( 3809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.306 Fit side-chains REVERT: A 358 ARG cc_start: 0.7668 (mtp-110) cc_final: 0.7199 (mtt90) REVERT: A 412 TYR cc_start: 0.8034 (t80) cc_final: 0.7730 (t80) REVERT: A 424 LEU cc_start: 0.5867 (OUTLIER) cc_final: 0.5518 (mt) outliers start: 12 outliers final: 9 residues processed: 47 average time/residue: 0.1038 time to fit residues: 6.4584 Evaluate side-chains 48 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.0060 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.153540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.132240 restraints weight = 3847.119| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.02 r_work: 0.3380 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2778 Z= 0.133 Angle : 0.608 14.675 3809 Z= 0.281 Chirality : 0.038 0.107 472 Planarity : 0.005 0.040 452 Dihedral : 6.061 40.485 384 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.42 % Allowed : 18.84 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.13 (0.43), residues: 351 helix: 1.85 (0.30), residues: 273 sheet: None (None), residues: 0 loop : -0.03 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 98 HIS 0.003 0.001 HIS A 335 PHE 0.014 0.001 PHE A 406 TYR 0.007 0.001 TYR A 412 ARG 0.001 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 195) hydrogen bonds : angle 3.71957 ( 582) covalent geometry : bond 0.00308 ( 2778) covalent geometry : angle 0.60778 ( 3809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.318 Fit side-chains REVERT: A 358 ARG cc_start: 0.7624 (mtp-110) cc_final: 0.7179 (mtt90) REVERT: A 412 TYR cc_start: 0.8006 (t80) cc_final: 0.7714 (t80) REVERT: A 424 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.5456 (mt) REVERT: A 447 MET cc_start: 0.8474 (mmm) cc_final: 0.8190 (tpt) outliers start: 10 outliers final: 8 residues processed: 46 average time/residue: 0.1321 time to fit residues: 8.2349 Evaluate side-chains 48 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.0060 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.157453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.136544 restraints weight = 3709.592| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.92 r_work: 0.3412 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2778 Z= 0.120 Angle : 0.579 12.625 3809 Z= 0.267 Chirality : 0.037 0.106 472 Planarity : 0.005 0.041 452 Dihedral : 5.994 41.249 384 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.74 % Allowed : 19.52 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.33 (0.44), residues: 351 helix: 1.99 (0.30), residues: 273 sheet: None (None), residues: 0 loop : 0.05 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 98 HIS 0.002 0.001 HIS A 335 PHE 0.013 0.001 PHE A 406 TYR 0.007 0.001 TYR A 412 ARG 0.001 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 195) hydrogen bonds : angle 3.61386 ( 582) covalent geometry : bond 0.00273 ( 2778) covalent geometry : angle 0.57893 ( 3809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.267 Fit side-chains REVERT: A 358 ARG cc_start: 0.7547 (mtp-110) cc_final: 0.7144 (mtt90) REVERT: A 412 TYR cc_start: 0.7936 (t80) cc_final: 0.7639 (t80) REVERT: A 424 LEU cc_start: 0.5719 (OUTLIER) cc_final: 0.5426 (mt) REVERT: A 447 MET cc_start: 0.8492 (mmm) cc_final: 0.8189 (tpt) outliers start: 8 outliers final: 7 residues processed: 46 average time/residue: 0.1024 time to fit residues: 6.2208 Evaluate side-chains 48 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.0370 overall best weight: 0.3458 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.158578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.137338 restraints weight = 3772.692| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.96 r_work: 0.3441 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2778 Z= 0.111 Angle : 0.566 11.994 3809 Z= 0.262 Chirality : 0.036 0.103 472 Planarity : 0.005 0.041 452 Dihedral : 5.927 43.273 384 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.74 % Allowed : 20.55 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.47 (0.43), residues: 351 helix: 2.08 (0.30), residues: 273 sheet: None (None), residues: 0 loop : 0.15 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 98 HIS 0.002 0.000 HIS A 6 PHE 0.012 0.001 PHE A 406 TYR 0.007 0.001 TYR A 412 ARG 0.000 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 195) hydrogen bonds : angle 3.60038 ( 582) covalent geometry : bond 0.00246 ( 2778) covalent geometry : angle 0.56628 ( 3809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.295 Fit side-chains REVERT: A 358 ARG cc_start: 0.7474 (mtp-110) cc_final: 0.7091 (mtt90) REVERT: A 412 TYR cc_start: 0.7882 (t80) cc_final: 0.7601 (t80) REVERT: A 424 LEU cc_start: 0.5643 (OUTLIER) cc_final: 0.5364 (mt) REVERT: A 447 MET cc_start: 0.8466 (mmm) cc_final: 0.8197 (tpt) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.1059 time to fit residues: 6.4278 Evaluate side-chains 45 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 0.0050 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.156754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135453 restraints weight = 3821.124| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.97 r_work: 0.3395 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2778 Z= 0.133 Angle : 0.607 12.114 3809 Z= 0.281 Chirality : 0.038 0.108 472 Planarity : 0.005 0.040 452 Dihedral : 5.957 40.566 384 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.40 % Allowed : 21.23 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.17 (0.44), residues: 351 helix: 1.81 (0.30), residues: 279 sheet: None (None), residues: 0 loop : 0.11 (0.72), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 98 HIS 0.003 0.001 HIS A 335 PHE 0.014 0.001 PHE A 406 TYR 0.007 0.001 TYR A 412 ARG 0.001 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 195) hydrogen bonds : angle 3.72498 ( 582) covalent geometry : bond 0.00312 ( 2778) covalent geometry : angle 0.60691 ( 3809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.246 Fit side-chains REVERT: A 358 ARG cc_start: 0.7527 (mtp-110) cc_final: 0.7117 (mtt90) REVERT: A 412 TYR cc_start: 0.7963 (t80) cc_final: 0.7647 (t80) REVERT: A 424 LEU cc_start: 0.5704 (OUTLIER) cc_final: 0.5428 (mt) REVERT: A 447 MET cc_start: 0.8485 (mmm) cc_final: 0.8213 (tpt) outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 0.1014 time to fit residues: 5.9385 Evaluate side-chains 46 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.155319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.134176 restraints weight = 3709.379| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.92 r_work: 0.3391 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2778 Z= 0.141 Angle : 0.612 11.980 3809 Z= 0.286 Chirality : 0.038 0.108 472 Planarity : 0.005 0.040 452 Dihedral : 6.017 40.433 384 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.08 % Allowed : 21.23 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.04 (0.43), residues: 351 helix: 1.71 (0.30), residues: 279 sheet: None (None), residues: 0 loop : 0.11 (0.72), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 98 HIS 0.003 0.001 HIS A 335 PHE 0.014 0.001 PHE A 406 TYR 0.008 0.001 TYR A 412 ARG 0.001 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 195) hydrogen bonds : angle 3.80742 ( 582) covalent geometry : bond 0.00336 ( 2778) covalent geometry : angle 0.61233 ( 3809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1874.90 seconds wall clock time: 32 minutes 55.27 seconds (1975.27 seconds total)