Starting phenix.real_space_refine on Wed Jul 1 21:51:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ex6_28652/07_2026/8ex6_28652.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ex6_28652/07_2026/8ex6_28652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ex6_28652/07_2026/8ex6_28652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ex6_28652/07_2026/8ex6_28652.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ex6_28652/07_2026/8ex6_28652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ex6_28652/07_2026/8ex6_28652.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 17 5.16 5 C 2120 2.51 5 N 531 2.21 5 O 553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3222 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3197 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 12, 'TRANS': 403} Chain breaks: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'S1P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.00, per 1000 atoms: 0.31 Number of scatterers: 3222 At special positions: 0 Unit cell: (72.039, 69.443, 83.721, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 1 15.00 O 553 8.00 N 531 7.00 C 2120 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: 0.30 Conformation dependent library (CDL) restraints added in 115.9 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 95.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 99 through 125 removed outlier: 4.663A pdb=" N VAL A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 136 through 165 removed outlier: 3.982A pdb=" N GLN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 3.526A pdb=" N ASP A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 186 Processing helix chain 'A' and resid 193 through 222 Proline residue: A 215 - end of helix removed outlier: 3.692A pdb=" N PHE A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 257 removed outlier: 4.400A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 4.018A pdb=" N GLN A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 264 Processing helix chain 'A' and resid 265 through 281 removed outlier: 4.068A pdb=" N LEU A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 312 through 348 Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 361 through 390 removed outlier: 4.259A pdb=" N VAL A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL A 379 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 421 removed outlier: 4.112A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.677A pdb=" N ALA A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 455 through 471 Processing helix chain 'A' and resid 474 through 490 removed outlier: 3.822A pdb=" N THR A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 506 through 539 removed outlier: 4.111A pdb=" N PHE A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N SER A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) 289 hydrogen bonds defined for protein. 855 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: 0.51 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 976 1.34 - 1.46: 554 1.46 - 1.57: 1738 1.57 - 1.69: 1 1.69 - 1.80: 26 Bond restraints: 3295 Sorted by residual: bond pdb=" C3 S1P A 601 " pdb=" O3 S1P A 601 " ideal model delta sigma weight residual 1.445 1.400 0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" C3 S1P A 601 " pdb=" C4 S1P A 601 " ideal model delta sigma weight residual 1.496 1.527 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" O1 S1P A 601 " pdb=" P22 S1P A 601 " ideal model delta sigma weight residual 1.677 1.647 0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C5 S1P A 601 " pdb=" C6 S1P A 601 " ideal model delta sigma weight residual 1.497 1.525 -0.028 2.00e-02 2.50e+03 2.03e+00 bond pdb=" C1 S1P A 601 " pdb=" O1 S1P A 601 " ideal model delta sigma weight residual 1.421 1.399 0.022 2.00e-02 2.50e+03 1.23e+00 ... (remaining 3290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4325 1.56 - 3.11: 92 3.11 - 4.67: 33 4.67 - 6.23: 16 6.23 - 7.78: 3 Bond angle restraints: 4469 Sorted by residual: angle pdb=" C GLY A 333 " pdb=" N MET A 334 " pdb=" CA MET A 334 " ideal model delta sigma weight residual 121.64 115.64 6.00 2.13e+00 2.20e-01 7.92e+00 angle pdb=" O1 S1P A 601 " pdb=" P22 S1P A 601 " pdb=" O24 S1P A 601 " ideal model delta sigma weight residual 101.67 109.45 -7.78 3.00e+00 1.11e-01 6.73e+00 angle pdb=" N PHE A 176 " pdb=" CA PHE A 176 " pdb=" CB PHE A 176 " ideal model delta sigma weight residual 110.39 114.93 -4.54 1.75e+00 3.27e-01 6.73e+00 angle pdb=" N LYS A 224 " pdb=" CA LYS A 224 " pdb=" C LYS A 224 " ideal model delta sigma weight residual 111.02 114.17 -3.15 1.22e+00 6.72e-01 6.67e+00 angle pdb=" C PHE A 177 " pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta sigma weight residual 120.68 116.32 4.36 1.70e+00 3.46e-01 6.58e+00 ... (remaining 4464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.61: 1851 30.61 - 61.22: 49 61.22 - 91.83: 4 91.83 - 122.44: 5 122.44 - 153.05: 2 Dihedral angle restraints: 1911 sinusoidal: 725 harmonic: 1186 Sorted by residual: dihedral pdb=" C11 S1P A 601 " pdb=" C10 S1P A 601 " pdb=" C9 S1P A 601 " pdb=" C8 S1P A 601 " ideal model delta sinusoidal sigma weight residual 65.14 -141.81 -153.05 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C3 S1P A 601 " pdb=" C1 S1P A 601 " pdb=" C2 S1P A 601 " pdb=" O1 S1P A 601 " ideal model delta sinusoidal sigma weight residual 52.36 -75.26 127.62 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" N2 S1P A 601 " pdb=" C1 S1P A 601 " pdb=" C2 S1P A 601 " pdb=" O1 S1P A 601 " ideal model delta sinusoidal sigma weight residual 286.07 164.80 121.27 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 1908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 342 0.036 - 0.071: 138 0.071 - 0.106: 34 0.106 - 0.142: 9 0.142 - 0.177: 2 Chirality restraints: 525 Sorted by residual: chirality pdb=" C2 S1P A 601 " pdb=" C1 S1P A 601 " pdb=" C3 S1P A 601 " pdb=" N2 S1P A 601 " both_signs ideal model delta sigma weight residual False -2.43 -2.60 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CA SER A 475 " pdb=" N SER A 475 " pdb=" C SER A 475 " pdb=" CB SER A 475 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CB VAL A 125 " pdb=" CA VAL A 125 " pdb=" CG1 VAL A 125 " pdb=" CG2 VAL A 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 522 not shown) Planarity restraints: 543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " 0.022 2.00e-02 2.50e+03 1.82e-02 8.28e+00 pdb=" CG TRP A 178 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 176 " -0.012 2.00e-02 2.50e+03 1.41e-02 3.46e+00 pdb=" CG PHE A 176 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 176 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 176 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 176 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 176 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 176 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 266 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 267 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " -0.019 5.00e-02 4.00e+02 ... (remaining 540 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 22 2.65 - 3.21: 3181 3.21 - 3.77: 5146 3.77 - 4.34: 6743 4.34 - 4.90: 11482 Nonbonded interactions: 26574 Sorted by model distance: nonbonded pdb=" OH TYR A 246 " pdb=" O GLY A 333 " model vdw 2.088 3.040 nonbonded pdb=" O GLY A 219 " pdb=" NH1 ARG A 227 " model vdw 2.262 3.120 nonbonded pdb=" OG1 THR A 373 " pdb=" OE1 GLU A 433 " model vdw 2.342 3.040 nonbonded pdb=" OD2 ASP A 128 " pdb=" NZ LYS A 253 " model vdw 2.355 3.120 nonbonded pdb=" O ILE A 486 " pdb=" OG SER A 489 " model vdw 2.395 3.040 ... (remaining 26569 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 group one per residue 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: 3.930 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.140 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.005 0.045 3295 Z= 0.216 Angle : 0.716 7.785 4469 Z= 0.371 Chirality : 0.042 0.177 525 Planarity : 0.004 0.034 543 Dihedral : 15.956 153.052 1151 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.43), residues: 410 helix: 1.97 (0.28), residues: 364 sheet: None (None), residues: 0 loop : 0.65 (1.07), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 456 TYR 0.011 0.001 TYR A 116 PHE 0.033 0.002 PHE A 176 TRP 0.050 0.002 TRP A 178 HIS 0.007 0.002 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.22 ( 3295) covalent geometry : angle 0.71583 / 0.37 ( 4469) hydrogen bonds : bond 0.12193 / 8.08 ( 289) hydrogen bonds : angle 5.42143 / 4.10 ( 855) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.116 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0514 time to fit residues: 2.5114 Evaluate side-chains 31 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.0770 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.166728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.144463 restraints weight = 3710.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147816 restraints weight = 2397.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.150021 restraints weight = 1790.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151292 restraints weight = 1469.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.152441 restraints weight = 1293.659| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3295 Z= 0.145 Angle : 0.559 7.780 4469 Z= 0.289 Chirality : 0.039 0.140 525 Planarity : 0.004 0.031 543 Dihedral : 12.348 140.252 471 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.19 % Allowed : 4.75 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.43), residues: 410 helix: 2.17 (0.27), residues: 367 sheet: None (None), residues: 0 loop : 1.40 (1.22), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 227 TYR 0.012 0.001 TYR A 116 PHE 0.014 0.001 PHE A 151 TRP 0.032 0.001 TRP A 178 HIS 0.006 0.002 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 3295) covalent geometry : angle 0.55906 / 0.29 ( 4469) hydrogen bonds : bond 0.04810 / 3.23 ( 289) hydrogen bonds : angle 4.41725 / 3.34 ( 855) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.114 Fit side-chains REVERT: A 439 ASN cc_start: 0.8502 (p0) cc_final: 0.8300 (p0) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.0635 time to fit residues: 3.0858 Evaluate side-chains 35 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.163257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.141161 restraints weight = 3769.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.144401 restraints weight = 2465.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.146486 restraints weight = 1852.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.148016 restraints weight = 1525.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148859 restraints weight = 1330.065| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3295 Z= 0.176 Angle : 0.581 8.416 4469 Z= 0.296 Chirality : 0.040 0.142 525 Planarity : 0.004 0.031 543 Dihedral : 9.667 88.738 471 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.48 % Allowed : 9.50 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.06 (0.43), residues: 410 helix: 2.14 (0.27), residues: 367 sheet: None (None), residues: 0 loop : 1.23 (1.22), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 227 TYR 0.011 0.001 TYR A 116 PHE 0.012 0.001 PHE A 327 TRP 0.036 0.002 TRP A 178 HIS 0.005 0.002 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 3295) covalent geometry : angle 0.58059 / 0.30 ( 4469) hydrogen bonds : bond 0.05116 / 3.46 ( 289) hydrogen bonds : angle 4.44457 / 3.35 ( 855) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.223 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.0502 time to fit residues: 2.6053 Evaluate side-chains 37 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 522 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.181335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162048 restraints weight = 3504.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.165163 restraints weight = 2296.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.167226 restraints weight = 1729.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.168414 restraints weight = 1420.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.169462 restraints weight = 1241.347| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3295 Z= 0.156 Angle : 0.542 7.895 4469 Z= 0.280 Chirality : 0.039 0.138 525 Planarity : 0.004 0.031 543 Dihedral : 8.630 86.194 471 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.48 % Allowed : 10.68 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.24 (0.42), residues: 410 helix: 2.24 (0.27), residues: 367 sheet: None (None), residues: 0 loop : 1.48 (1.25), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 227 TYR 0.011 0.001 TYR A 116 PHE 0.013 0.001 PHE A 151 TRP 0.036 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 3295) covalent geometry : angle 0.54231 / 0.28 ( 4469) hydrogen bonds : bond 0.04792 / 3.24 ( 289) hydrogen bonds : angle 4.40560 / 3.34 ( 855) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.116 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 0.0600 time to fit residues: 2.9435 Evaluate side-chains 38 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 522 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.181754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.161333 restraints weight = 3486.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.164983 restraints weight = 2161.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.167330 restraints weight = 1561.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.168722 restraints weight = 1254.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.169775 restraints weight = 1077.841| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3295 Z= 0.151 Angle : 0.542 7.700 4469 Z= 0.278 Chirality : 0.040 0.139 525 Planarity : 0.004 0.030 543 Dihedral : 8.412 88.228 471 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.19 % Allowed : 11.57 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.43), residues: 410 helix: 2.32 (0.27), residues: 367 sheet: None (None), residues: 0 loop : 1.66 (1.27), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 227 TYR 0.011 0.001 TYR A 116 PHE 0.014 0.001 PHE A 151 TRP 0.036 0.001 TRP A 178 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 3295) covalent geometry : angle 0.54202 / 0.28 ( 4469) hydrogen bonds : bond 0.04692 / 3.18 ( 289) hydrogen bonds : angle 4.38504 / 3.33 ( 855) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.117 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 0.0585 time to fit residues: 2.7432 Evaluate side-chains 35 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 522 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.182161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163336 restraints weight = 3524.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.166403 restraints weight = 2308.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.168412 restraints weight = 1731.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.169550 restraints weight = 1426.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.170577 restraints weight = 1251.239| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3295 Z= 0.146 Angle : 0.519 6.401 4469 Z= 0.273 Chirality : 0.039 0.137 525 Planarity : 0.004 0.030 543 Dihedral : 8.259 89.962 471 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.59 % Allowed : 12.17 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.45 (0.42), residues: 410 helix: 2.37 (0.27), residues: 367 sheet: None (None), residues: 0 loop : 1.72 (1.26), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 227 TYR 0.011 0.001 TYR A 116 PHE 0.014 0.001 PHE A 151 TRP 0.036 0.001 TRP A 178 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 3295) covalent geometry : angle 0.51914 / 0.27 ( 4469) hydrogen bonds : bond 0.04584 / 3.10 ( 289) hydrogen bonds : angle 4.35019 / 3.29 ( 855) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.071 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.0349 time to fit residues: 1.5840 Evaluate side-chains 33 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.138005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.117697 restraints weight = 3707.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117869 restraints weight = 2895.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.118455 restraints weight = 2594.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.120528 restraints weight = 2276.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.120553 restraints weight = 1968.724| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3295 Z= 0.180 Angle : 0.579 9.808 4469 Z= 0.297 Chirality : 0.041 0.140 525 Planarity : 0.004 0.031 543 Dihedral : 8.321 89.311 471 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.89 % Allowed : 13.35 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.26 (0.43), residues: 410 helix: 2.24 (0.27), residues: 367 sheet: None (None), residues: 0 loop : 1.61 (1.27), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 227 TYR 0.011 0.001 TYR A 116 PHE 0.014 0.001 PHE A 151 TRP 0.037 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 3295) covalent geometry : angle 0.57886 / 0.30 ( 4469) hydrogen bonds : bond 0.05035 / 3.41 ( 289) hydrogen bonds : angle 4.45603 / 3.37 ( 855) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.115 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.0618 time to fit residues: 2.8580 Evaluate side-chains 33 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 19 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.181129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.160503 restraints weight = 3585.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.164254 restraints weight = 2173.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.166670 restraints weight = 1555.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.168296 restraints weight = 1231.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.169167 restraints weight = 1039.576| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3295 Z= 0.134 Angle : 0.526 8.950 4469 Z= 0.272 Chirality : 0.039 0.140 525 Planarity : 0.004 0.029 543 Dihedral : 7.999 86.923 471 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.19 % Allowed : 13.06 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.52 (0.42), residues: 410 helix: 2.41 (0.27), residues: 367 sheet: None (None), residues: 0 loop : 1.77 (1.26), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 227 TYR 0.012 0.001 TYR A 116 PHE 0.014 0.001 PHE A 151 TRP 0.035 0.001 TRP A 178 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 3295) covalent geometry : angle 0.52574 / 0.27 ( 4469) hydrogen bonds : bond 0.04364 / 2.95 ( 289) hydrogen bonds : angle 4.33675 / 3.28 ( 855) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.111 Fit side-chains REVERT: A 375 PHE cc_start: 0.7860 (m-10) cc_final: 0.7622 (m-10) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.0501 time to fit residues: 2.4360 Evaluate side-chains 34 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.141100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.119681 restraints weight = 3702.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.122577 restraints weight = 2465.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.124717 restraints weight = 1854.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.126085 restraints weight = 1520.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.127017 restraints weight = 1316.097| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3295 Z= 0.147 Angle : 0.544 8.886 4469 Z= 0.283 Chirality : 0.040 0.150 525 Planarity : 0.004 0.030 543 Dihedral : 7.973 86.028 471 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.59 % Allowed : 13.65 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.42), residues: 410 helix: 2.39 (0.27), residues: 367 sheet: None (None), residues: 0 loop : 1.73 (1.26), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 227 TYR 0.011 0.001 TYR A 116 PHE 0.015 0.001 PHE A 151 TRP 0.036 0.001 TRP A 178 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 3295) covalent geometry : angle 0.54426 / 0.28 ( 4469) hydrogen bonds : bond 0.04534 / 3.06 ( 289) hydrogen bonds : angle 4.37231 / 3.31 ( 855) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.069 Fit side-chains REVERT: A 375 PHE cc_start: 0.7856 (m-10) cc_final: 0.7627 (m-10) outliers start: 2 outliers final: 2 residues processed: 31 average time/residue: 0.0339 time to fit residues: 1.5145 Evaluate side-chains 29 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.181052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.161818 restraints weight = 3591.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.164860 restraints weight = 2362.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.167048 restraints weight = 1761.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.168248 restraints weight = 1438.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.169230 restraints weight = 1255.034| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3295 Z= 0.164 Angle : 0.560 9.039 4469 Z= 0.292 Chirality : 0.040 0.161 525 Planarity : 0.004 0.030 543 Dihedral : 7.970 85.160 471 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.59 % Allowed : 13.95 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.34 (0.43), residues: 410 helix: 2.29 (0.27), residues: 367 sheet: None (None), residues: 0 loop : 1.68 (1.27), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 227 TYR 0.011 0.001 TYR A 116 PHE 0.013 0.001 PHE A 498 TRP 0.036 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 3295) covalent geometry : angle 0.56043 / 0.29 ( 4469) hydrogen bonds : bond 0.04768 / 3.22 ( 289) hydrogen bonds : angle 4.43877 / 3.36 ( 855) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.112 Fit side-chains REVERT: A 375 PHE cc_start: 0.7849 (m-10) cc_final: 0.7635 (m-10) outliers start: 2 outliers final: 2 residues processed: 32 average time/residue: 0.0533 time to fit residues: 2.2911 Evaluate side-chains 33 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 178 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 0.0270 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.183210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.162884 restraints weight = 3575.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.166610 restraints weight = 2178.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.168971 restraints weight = 1556.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.170458 restraints weight = 1234.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.171535 restraints weight = 1050.943| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3295 Z= 0.143 Angle : 0.541 8.989 4469 Z= 0.282 Chirality : 0.040 0.156 525 Planarity : 0.004 0.030 543 Dihedral : 7.813 83.616 471 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.59 % Allowed : 13.65 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.41 (0.43), residues: 410 helix: 2.34 (0.27), residues: 367 sheet: None (None), residues: 0 loop : 1.73 (1.28), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 227 TYR 0.012 0.001 TYR A 116 PHE 0.015 0.001 PHE A 151 TRP 0.036 0.001 TRP A 178 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 3295) covalent geometry : angle 0.54071 / 0.28 ( 4469) hydrogen bonds : bond 0.04457 / 3.00 ( 289) hydrogen bonds : angle 4.38720 / 3.32 ( 855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 790.10 seconds wall clock time: 14 minutes 24.03 seconds (864.03 seconds total)