Starting phenix.real_space_refine on Mon Feb 10 23:58:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8goe_34176/02_2025/8goe_34176_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8goe_34176/02_2025/8goe_34176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8goe_34176/02_2025/8goe_34176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8goe_34176/02_2025/8goe_34176.map" model { file = "/net/cci-nas-00/data/ceres_data/8goe_34176/02_2025/8goe_34176_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8goe_34176/02_2025/8goe_34176_neut.cif" } resolution = 3.0 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= 0.000 sd= 0.005 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 10 5.16 5 C 2204 2.51 5 N 555 2.21 5 O 554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 3323 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3290 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 407, 3268 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 14, 'TRANS': 392} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 407, 3268 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 14, 'TRANS': 392} Chain breaks: 1 bond proxies already assigned to first conformer: 3334 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 1, 33 Unusual residues: {'THH': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 133 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 133 " occ=0.50 residue: pdb=" N AARG A 208 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 208 " occ=0.50 Time building chain proxies: 4.35, per 1000 atoms: 1.31 Number of scatterers: 3323 At special positions: 0 Unit cell: (78, 73, 67, 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 10 16.00 O 554 8.00 N 555 7.00 C 2204 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: 0.92 Conformation dependent library (CDL) restraints added in 740.5 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB THH A 601 " Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 82.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 25 through 39 removed outlier: 3.754A pdb=" N TYR A 31 " --> pdb=" O HIS A 27 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 34 " --> pdb=" O CYS A 30 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.778A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.662A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 113 removed outlier: 3.559A pdb=" N LEU A 111 " --> pdb=" O TRP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.596A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 removed outlier: 4.280A pdb=" N SER A 137 " --> pdb=" O AARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 144 removed outlier: 3.611A pdb=" N SER A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 176 removed outlier: 4.722A pdb=" N GLN A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ARG A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 202 removed outlier: 3.741A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 257 Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.772A pdb=" N ARG A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.741A pdb=" N LEU A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 286 removed outlier: 3.552A pdb=" N VAL A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 300 through 304 removed outlier: 3.534A pdb=" N ARG A 303 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 325 removed outlier: 3.624A pdb=" N SER A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 388 removed outlier: 3.517A pdb=" N PHE A 369 " --> pdb=" O CYS A 365 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 392 through 418 Processing helix chain 'A' and resid 427 through 453 removed outlier: 3.607A pdb=" N LEU A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 642 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: 1.03 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 472 1.31 - 1.43: 1057 1.43 - 1.56: 1871 1.56 - 1.68: 1 1.68 - 1.81: 16 Bond restraints: 3417 Sorted by residual: bond pdb=" C4 THH A 601 " pdb=" O4 THH A 601 " ideal model delta sigma weight residual 1.347 1.184 0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" N8 THH A 601 " pdb=" C8AATHH A 601 " ideal model delta sigma weight residual 1.351 1.508 -0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" N THH A 601 " pdb=" C THH A 601 " ideal model delta sigma weight residual 1.346 1.479 -0.133 2.00e-02 2.50e+03 4.45e+01 bond pdb=" N5 THH A 601 " pdb=" C4AATHH A 601 " ideal model delta sigma weight residual 1.419 1.504 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C15 THH A 601 " pdb=" N10 THH A 601 " ideal model delta sigma weight residual 1.379 1.460 -0.081 2.00e-02 2.50e+03 1.65e+01 ... (remaining 3412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 4505 1.96 - 3.91: 117 3.91 - 5.87: 24 5.87 - 7.83: 12 7.83 - 9.79: 1 Bond angle restraints: 4659 Sorted by residual: angle pdb=" C TYR A 92 " pdb=" CA TYR A 92 " pdb=" CB TYR A 92 " ideal model delta sigma weight residual 111.23 101.44 9.79 1.63e+00 3.76e-01 3.60e+01 angle pdb=" N GLN A 120 " pdb=" CA GLN A 120 " pdb=" C GLN A 120 " ideal model delta sigma weight residual 111.36 105.80 5.56 1.09e+00 8.42e-01 2.60e+01 angle pdb=" CA VAL A 327 " pdb=" CB VAL A 327 " pdb=" CG1 VAL A 327 " ideal model delta sigma weight residual 110.40 115.30 -4.90 1.70e+00 3.46e-01 8.30e+00 angle pdb=" N THR A 69 " pdb=" CA THR A 69 " pdb=" C THR A 69 " ideal model delta sigma weight residual 109.81 115.98 -6.17 2.21e+00 2.05e-01 7.79e+00 angle pdb=" CA THR A 49 " pdb=" C THR A 49 " pdb=" N PRO A 50 " ideal model delta sigma weight residual 118.44 122.66 -4.22 1.59e+00 3.96e-01 7.06e+00 ... (remaining 4654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.92: 1687 11.92 - 23.84: 206 23.84 - 35.75: 57 35.75 - 47.67: 15 47.67 - 59.59: 18 Dihedral angle restraints: 1983 sinusoidal: 777 harmonic: 1206 Sorted by residual: dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LEU A 452 " pdb=" C LEU A 452 " pdb=" N ASP A 453 " pdb=" CA ASP A 453 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CG ARG A 253 " pdb=" CD ARG A 253 " pdb=" NE ARG A 253 " pdb=" CZ ARG A 253 " ideal model delta sinusoidal sigma weight residual 90.00 133.63 -43.63 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 1980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 345 0.039 - 0.077: 151 0.077 - 0.116: 29 0.116 - 0.155: 8 0.155 - 0.193: 4 Chirality restraints: 537 Sorted by residual: chirality pdb=" CA ARG A 42 " pdb=" N ARG A 42 " pdb=" C ARG A 42 " pdb=" CB ARG A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CA LEU A 121 " pdb=" N LEU A 121 " pdb=" C LEU A 121 " pdb=" CB LEU A 121 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA MET A 122 " pdb=" N MET A 122 " pdb=" C MET A 122 " pdb=" CB MET A 122 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.17 2.00e-01 2.50e+01 7.65e-01 ... (remaining 534 not shown) Planarity restraints: 565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " 0.041 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO A 70 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 41 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C ILE A 41 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE A 41 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 42 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " -0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 82 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " -0.030 5.00e-02 4.00e+02 ... (remaining 562 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 997 2.80 - 3.32: 2989 3.32 - 3.85: 5671 3.85 - 4.37: 7086 4.37 - 4.90: 11737 Nonbonded interactions: 28480 Sorted by model distance: nonbonded pdb=" NH2 ARG A 42 " pdb=" OE2 GLU A 45 " model vdw 2.273 3.120 nonbonded pdb=" O VAL A 304 " pdb=" OH TYR A 366 " model vdw 2.286 3.040 nonbonded pdb=" O VAL A 64 " pdb=" OG1 THR A 69 " model vdw 2.296 3.040 nonbonded pdb=" O LEU A 32 " pdb=" OH TYR A 136 " model vdw 2.301 3.040 nonbonded pdb=" OE2 GLU A 45 " pdb=" OH TYR A 126 " model vdw 2.313 3.040 ... (remaining 28475 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=0.50 max=1.00 mean=0.99 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 15.270 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 0.163 3417 Z= 0.511 Angle : 0.851 9.785 4659 Z= 0.468 Chirality : 0.046 0.193 537 Planarity : 0.006 0.061 565 Dihedral : 13.131 59.587 1209 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.57 % Allowed : 8.50 % Favored : 90.93 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.19 (0.23), residues: 409 helix: -4.26 (0.12), residues: 323 sheet: None (None), residues: 0 loop : -2.02 (0.53), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.001 HIS A 358 PHE 0.010 0.002 PHE A 37 TYR 0.008 0.001 TYR A 92 ARG 0.004 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.343 Fit side-chains REVERT: A 88 ASP cc_start: 0.8379 (t70) cc_final: 0.8063 (t70) REVERT: A 294 GLU cc_start: 0.8068 (tt0) cc_final: 0.7688 (tt0) REVERT: A 445 ILE cc_start: 0.8561 (mt) cc_final: 0.8268 (mt) REVERT: A 452 LEU cc_start: 0.7280 (mt) cc_final: 0.7038 (mt) outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 1.0621 time to fit residues: 59.3812 Evaluate side-chains 36 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 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 99 GLN A 266 GLN A 277 ASN A 377 GLN A 431 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.098652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.079947 restraints weight = 14393.956| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.83 r_work: 0.2613 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3417 Z= 0.201 Angle : 0.566 9.087 4659 Z= 0.293 Chirality : 0.038 0.105 537 Planarity : 0.005 0.036 565 Dihedral : 7.466 57.705 493 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.57 % Allowed : 10.20 % Favored : 89.24 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.34), residues: 409 helix: -1.53 (0.24), residues: 322 sheet: None (None), residues: 0 loop : -1.74 (0.55), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.015 0.001 PHE A 372 TYR 0.010 0.001 TYR A 149 ARG 0.004 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.6947 (mm) REVERT: A 294 GLU cc_start: 0.8354 (tt0) cc_final: 0.7953 (tt0) REVERT: A 452 LEU cc_start: 0.6892 (mt) cc_final: 0.6671 (mt) outliers start: 2 outliers final: 0 residues processed: 40 average time/residue: 0.8960 time to fit residues: 37.5281 Evaluate side-chains 37 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 0.2980 chunk 16 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3060 r_free = 0.3060 target = 0.098404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.079439 restraints weight = 16124.433| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.93 r_work: 0.2614 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3417 Z= 0.180 Angle : 0.516 7.890 4659 Z= 0.260 Chirality : 0.037 0.108 537 Planarity : 0.004 0.029 565 Dihedral : 6.630 49.726 492 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.13 % Allowed : 10.48 % Favored : 88.39 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.39), residues: 409 helix: 0.08 (0.28), residues: 317 sheet: None (None), residues: 0 loop : -1.32 (0.54), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.001 HIS A 355 PHE 0.024 0.001 PHE A 322 TYR 0.008 0.001 TYR A 149 ARG 0.003 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.7531 (mtt180) cc_final: 0.6732 (mmm160) REVERT: A 161 LEU cc_start: 0.7682 (pp) cc_final: 0.7156 (mm) REVERT: A 294 GLU cc_start: 0.8472 (tt0) cc_final: 0.8054 (tt0) REVERT: A 452 LEU cc_start: 0.6920 (mt) cc_final: 0.6705 (mt) outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 1.0425 time to fit residues: 47.7667 Evaluate side-chains 39 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 175 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.095984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.075824 restraints weight = 20406.828| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.27 r_work: 0.2543 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3417 Z= 0.272 Angle : 0.557 9.023 4659 Z= 0.278 Chirality : 0.040 0.122 537 Planarity : 0.003 0.026 565 Dihedral : 6.559 46.102 492 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.13 % Allowed : 12.46 % Favored : 86.40 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.40), residues: 409 helix: 0.47 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.12 (0.57), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.013 0.001 PHE A 372 TYR 0.011 0.001 TYR A 149 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.338 Fit side-chains REVERT: A 161 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7375 (mp) REVERT: A 294 GLU cc_start: 0.8702 (tt0) cc_final: 0.8244 (tt0) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.9078 time to fit residues: 35.2985 Evaluate side-chains 37 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 251 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 22 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3057 r_free = 0.3057 target = 0.098286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.078069 restraints weight = 20857.160| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.39 r_work: 0.2573 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3417 Z= 0.180 Angle : 0.515 9.591 4659 Z= 0.254 Chirality : 0.038 0.110 537 Planarity : 0.003 0.025 565 Dihedral : 6.124 42.316 492 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.85 % Allowed : 11.90 % Favored : 87.25 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.41), residues: 409 helix: 0.86 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -0.83 (0.60), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.001 HIS A 355 PHE 0.025 0.001 PHE A 322 TYR 0.009 0.001 TYR A 149 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.350 Fit side-chains REVERT: A 161 LEU cc_start: 0.7594 (pp) cc_final: 0.7158 (mm) REVERT: A 294 GLU cc_start: 0.8599 (tt0) cc_final: 0.8242 (tt0) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.8961 time to fit residues: 33.7339 Evaluate side-chains 35 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3043 r_free = 0.3043 target = 0.097985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.076892 restraints weight = 21509.373| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.73 r_work: 0.2757 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3417 Z= 0.211 Angle : 0.532 9.059 4659 Z= 0.263 Chirality : 0.039 0.113 537 Planarity : 0.003 0.040 565 Dihedral : 6.049 40.457 492 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.42 % Allowed : 11.90 % Favored : 86.69 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.41), residues: 409 helix: 0.99 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -0.73 (0.62), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.013 0.001 PHE A 372 TYR 0.010 0.001 TYR A 149 ARG 0.009 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.328 Fit side-chains REVERT: A 161 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7266 (mm) REVERT: A 256 ARG cc_start: 0.7629 (ttp80) cc_final: 0.6827 (mtm-85) REVERT: A 294 GLU cc_start: 0.8684 (tt0) cc_final: 0.8337 (tt0) outliers start: 5 outliers final: 3 residues processed: 40 average time/residue: 1.0121 time to fit residues: 42.2150 Evaluate side-chains 39 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3140 r_free = 0.3140 target = 0.104017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.084857 restraints weight = 14041.472| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.60 r_work: 0.2602 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3417 Z= 0.242 Angle : 0.547 10.044 4659 Z= 0.270 Chirality : 0.039 0.116 537 Planarity : 0.004 0.034 565 Dihedral : 6.082 39.896 492 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.13 % Allowed : 11.90 % Favored : 86.97 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.41), residues: 409 helix: 1.06 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -0.72 (0.63), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.026 0.001 PHE A 322 TYR 0.010 0.001 TYR A 149 ARG 0.008 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7242 (mm) REVERT: A 294 GLU cc_start: 0.8558 (tt0) cc_final: 0.8198 (tt0) REVERT: A 330 ARG cc_start: 0.7819 (mtm110) cc_final: 0.7602 (mtm-85) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.9774 time to fit residues: 37.7659 Evaluate side-chains 36 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3028 r_free = 0.3028 target = 0.096987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.075938 restraints weight = 21622.036| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.71 r_work: 0.2529 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3417 Z= 0.247 Angle : 0.550 9.547 4659 Z= 0.271 Chirality : 0.040 0.114 537 Planarity : 0.003 0.028 565 Dihedral : 6.041 39.669 492 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.13 % Allowed : 12.46 % Favored : 86.40 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.41), residues: 409 helix: 1.18 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -0.74 (0.63), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.012 0.001 PHE A 372 TYR 0.010 0.001 TYR A 149 ARG 0.007 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.376 Fit side-chains REVERT: A 161 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7248 (mm) REVERT: A 294 GLU cc_start: 0.8644 (tt0) cc_final: 0.8246 (tt0) outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 0.9832 time to fit residues: 39.0449 Evaluate side-chains 38 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.098689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.078790 restraints weight = 16973.695| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.05 r_work: 0.2589 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3417 Z= 0.193 Angle : 0.529 10.531 4659 Z= 0.259 Chirality : 0.039 0.110 537 Planarity : 0.003 0.030 565 Dihedral : 5.768 37.342 492 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.57 % Allowed : 13.03 % Favored : 86.40 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.42), residues: 409 helix: 1.36 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -0.69 (0.62), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.028 0.001 PHE A 322 TYR 0.011 0.001 TYR A 155 ARG 0.007 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.360 Fit side-chains REVERT: A 161 LEU cc_start: 0.7589 (pp) cc_final: 0.7142 (mm) REVERT: A 294 GLU cc_start: 0.8548 (tt0) cc_final: 0.8149 (tt0) outliers start: 2 outliers final: 2 residues processed: 37 average time/residue: 0.9894 time to fit residues: 38.1964 Evaluate side-chains 37 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3035 r_free = 0.3035 target = 0.097459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.077573 restraints weight = 17251.738| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.17 r_work: 0.2570 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3417 Z= 0.250 Angle : 0.567 9.877 4659 Z= 0.279 Chirality : 0.039 0.114 537 Planarity : 0.005 0.077 565 Dihedral : 5.853 37.211 492 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.85 % Allowed : 12.75 % Favored : 86.40 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.41), residues: 409 helix: 1.34 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -0.68 (0.62), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.012 0.001 PHE A 372 TYR 0.011 0.001 TYR A 149 ARG 0.020 0.001 ARG A 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.347 Fit side-chains REVERT: A 161 LEU cc_start: 0.7779 (pp) cc_final: 0.7327 (mm) REVERT: A 294 GLU cc_start: 0.8621 (tt0) cc_final: 0.8193 (tt0) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.8801 time to fit residues: 34.0937 Evaluate side-chains 36 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 0.0070 chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.3047 r_free = 0.3047 target = 0.098276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.078543 restraints weight = 16163.196| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.06 r_work: 0.2767 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3417 Z= 0.209 Angle : 0.547 9.525 4659 Z= 0.269 Chirality : 0.039 0.110 537 Planarity : 0.005 0.087 565 Dihedral : 5.756 36.773 492 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.85 % Allowed : 12.75 % Favored : 86.40 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.42), residues: 409 helix: 1.41 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -0.65 (0.62), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.027 0.001 PHE A 322 TYR 0.013 0.001 TYR A 155 ARG 0.019 0.001 ARG A 456 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2274.04 seconds wall clock time: 41 minutes 12.07 seconds (2472.07 seconds total)