Starting phenix.real_space_refine on Tue Aug 4 12:55:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qcs_18334/08_2026/8qcs_18334.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qcs_18334/08_2026/8qcs_18334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qcs_18334/08_2026/8qcs_18334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qcs_18334/08_2026/8qcs_18334.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qcs_18334/08_2026/8qcs_18334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qcs_18334/08_2026/8qcs_18334.map" } resolution = 2.9 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= 0.003 sd= 0.097 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 18 5.16 5 C 2156 2.51 5 N 500 2.21 5 O 567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3241 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3241 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 17, 'TRANS': 399} Time building chain proxies: 1.11, per 1000 atoms: 0.34 Number of scatterers: 3241 At special positions: 0 Unit cell: (80.22, 55.008, 65.322, 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 18 16.00 O 567 8.00 N 500 7.00 C 2156 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: 0.27 Conformation dependent library (CDL) restraints added in 136.7 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 90.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 105 through 127 removed outlier: 4.213A pdb=" N VAL A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 removed outlier: 4.068A pdb=" N GLY A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.719A pdb=" N ILE A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.722A pdb=" N LEU A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.712A pdb=" N THR A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 193 " --> pdb=" O TRP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 219 removed outlier: 3.555A pdb=" N THR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 4.349A pdb=" N ARG A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.502A pdb=" N THR A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 266 through 296 Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.777A pdb=" N ASP A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 319 removed outlier: 6.226A pdb=" N GLU A 317 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU A 318 " --> pdb=" O PRO A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 329 removed outlier: 3.542A pdb=" N PHE A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 363 removed outlier: 3.709A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 393 removed outlier: 4.112A pdb=" N GLY A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASP A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 418 removed outlier: 3.518A pdb=" N MET A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 424 through 440 removed outlier: 3.721A pdb=" N VAL A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 453 Processing helix chain 'A' and resid 458 through 489 removed outlier: 3.768A pdb=" N SER A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.556A pdb=" N LEU A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) 255 hydrogen bonds defined for protein. 756 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: 0.43 Time building geometry restraints manager: 0.39 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: 961 1.34 - 1.46: 641 1.46 - 1.57: 1693 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 3323 Sorted by residual: bond pdb=" N ILE A 427 " pdb=" CA ILE A 427 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.52e+00 bond pdb=" N GLN A 308 " pdb=" CA GLN A 308 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.30e-02 5.92e+03 5.28e+00 bond pdb=" N ASP A 169 " pdb=" CA ASP A 169 " ideal model delta sigma weight residual 1.457 1.486 -0.030 1.33e-02 5.65e+03 4.95e+00 bond pdb=" CB GLN A 306 " pdb=" CG GLN A 306 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" C ILE A 427 " pdb=" N VAL A 428 " ideal model delta sigma weight residual 1.335 1.324 0.011 1.20e-02 6.94e+03 8.92e-01 ... (remaining 3318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 4444 1.69 - 3.39: 66 3.39 - 5.08: 16 5.08 - 6.77: 7 6.77 - 8.47: 1 Bond angle restraints: 4534 Sorted by residual: angle pdb=" C ALA A 307 " pdb=" N GLN A 308 " pdb=" CA GLN A 308 " ideal model delta sigma weight residual 120.68 115.80 4.88 1.70e+00 3.46e-01 8.23e+00 angle pdb=" N GLN A 308 " pdb=" CA GLN A 308 " pdb=" C GLN A 308 " ideal model delta sigma weight residual 112.23 108.88 3.35 1.26e+00 6.30e-01 7.09e+00 angle pdb=" N LEU A 220 " pdb=" CA LEU A 220 " pdb=" C LEU A 220 " ideal model delta sigma weight residual 109.81 115.56 -5.75 2.21e+00 2.05e-01 6.76e+00 angle pdb=" N LYS A 396 " pdb=" CA LYS A 396 " pdb=" C LYS A 396 " ideal model delta sigma weight residual 108.34 111.55 -3.21 1.31e+00 5.83e-01 6.02e+00 angle pdb=" CA LEU A 269 " pdb=" CB LEU A 269 " pdb=" CG LEU A 269 " ideal model delta sigma weight residual 116.30 124.77 -8.47 3.50e+00 8.16e-02 5.85e+00 ... (remaining 4529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 1697 17.51 - 35.02: 168 35.02 - 52.53: 34 52.53 - 70.05: 13 70.05 - 87.56: 2 Dihedral angle restraints: 1914 sinusoidal: 714 harmonic: 1200 Sorted by residual: dihedral pdb=" CA ASP A 421 " pdb=" CB ASP A 421 " pdb=" CG ASP A 421 " pdb=" OD1 ASP A 421 " ideal model delta sinusoidal sigma weight residual -30.00 -86.73 56.73 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA TYR A 117 " pdb=" C TYR A 117 " pdb=" N SER A 118 " pdb=" CA SER A 118 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA THR A 440 " pdb=" C THR A 440 " pdb=" N GLY A 441 " pdb=" CA GLY A 441 " ideal model delta harmonic sigma weight residual 180.00 164.17 15.83 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 1911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 316 0.026 - 0.051: 130 0.051 - 0.077: 66 0.077 - 0.102: 23 0.102 - 0.128: 8 Chirality restraints: 543 Sorted by residual: chirality pdb=" CA ILE A 427 " pdb=" N ILE A 427 " pdb=" C ILE A 427 " pdb=" CB ILE A 427 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" C PRO A 221 " pdb=" CB PRO A 221 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.15e-01 chirality pdb=" CA TYR A 117 " pdb=" N TYR A 117 " pdb=" C TYR A 117 " pdb=" CB TYR A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.02e-01 ... (remaining 540 not shown) Planarity restraints: 550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 443 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO A 444 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 444 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 444 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 255 " -0.020 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO A 256 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 256 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 256 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 256 " 0.018 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO A 257 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " 0.015 5.00e-02 4.00e+02 ... (remaining 547 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1003 2.82 - 3.34: 3277 3.34 - 3.86: 5409 3.86 - 4.38: 6478 4.38 - 4.90: 10937 Nonbonded interactions: 27104 Sorted by model distance: nonbonded pdb=" ND2 ASN A 262 " pdb=" OE1 GLU A 367 " model vdw 2.301 3.120 nonbonded pdb=" O ILE A 415 " pdb=" OG1 THR A 419 " model vdw 2.380 3.040 nonbonded pdb=" OH TYR A 319 " pdb=" OG SER A 458 " model vdw 2.383 3.040 nonbonded pdb=" O GLY A 504 " pdb=" OG1 THR A 508 " model vdw 2.419 3.040 nonbonded pdb=" NE1 TRP A 189 " pdb=" OG1 THR A 286 " model vdw 2.424 3.120 ... (remaining 27099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.620 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:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3323 Z= 0.136 Angle : 0.571 8.467 4534 Z= 0.294 Chirality : 0.038 0.128 543 Planarity : 0.003 0.034 550 Dihedral : 15.225 87.558 1150 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 20.11 % Favored : 79.89 % 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: 0.62 (0.39), residues: 415 helix: 0.91 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -1.18 (0.58), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 107 TYR 0.016 0.001 TYR A 117 PHE 0.008 0.001 PHE A 162 TRP 0.006 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 3323) covalent geometry : angle 0.57116 / 0.29 ( 4534) hydrogen bonds : bond 0.24584 / 16.26 ( 255) hydrogen bonds : angle 7.70171 / 5.37 ( 756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.139 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.6230 time to fit residues: 25.6579 Evaluate side-chains 37 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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: 3.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 369 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.105514 restraints weight = 4136.655| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.21 r_work: 0.3058 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3323 Z= 0.146 Angle : 0.617 8.103 4534 Z= 0.315 Chirality : 0.040 0.153 543 Planarity : 0.004 0.030 550 Dihedral : 4.142 15.287 446 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.70 % Allowed : 18.70 % Favored : 79.60 % 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: 1.55 (0.41), residues: 415 helix: 1.67 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -1.69 (0.58), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 107 TYR 0.025 0.001 TYR A 117 PHE 0.010 0.001 PHE A 496 TRP 0.010 0.001 TRP A 500 HIS 0.001 0.000 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 3323) covalent geometry : angle 0.61706 / 0.32 ( 4534) hydrogen bonds : bond 0.05183 / 3.31 ( 255) hydrogen bonds : angle 4.85555 / 3.38 ( 756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.117 Fit side-chains REVERT: A 136 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6508 (mt-10) REVERT: A 169 ASP cc_start: 0.7603 (m-30) cc_final: 0.7225 (m-30) REVERT: A 277 MET cc_start: 0.7864 (ttp) cc_final: 0.7660 (ttm) REVERT: A 390 LEU cc_start: 0.7484 (mt) cc_final: 0.6722 (tt) REVERT: A 409 SER cc_start: 0.9063 (t) cc_final: 0.8809 (m) outliers start: 6 outliers final: 0 residues processed: 53 average time/residue: 0.4357 time to fit residues: 23.8384 Evaluate side-chains 42 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.133511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104758 restraints weight = 4084.355| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.18 r_work: 0.3053 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3323 Z= 0.145 Angle : 0.588 7.278 4534 Z= 0.299 Chirality : 0.040 0.149 543 Planarity : 0.004 0.030 550 Dihedral : 4.065 15.223 446 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.55 % Allowed : 19.26 % Favored : 78.19 % 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: 1.80 (0.41), residues: 415 helix: 1.90 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.79 (0.57), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.025 0.001 TYR A 117 PHE 0.010 0.001 PHE A 496 TRP 0.009 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 3323) covalent geometry : angle 0.58774 / 0.30 ( 4534) hydrogen bonds : bond 0.04717 / 3.03 ( 255) hydrogen bonds : angle 4.58044 / 3.19 ( 756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.072 Fit side-chains REVERT: A 136 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6391 (mt-10) REVERT: A 277 MET cc_start: 0.7835 (ttp) cc_final: 0.7616 (ttm) REVERT: A 390 LEU cc_start: 0.7580 (mt) cc_final: 0.6799 (tt) REVERT: A 409 SER cc_start: 0.9044 (t) cc_final: 0.8811 (m) outliers start: 9 outliers final: 1 residues processed: 48 average time/residue: 0.4503 time to fit residues: 22.2931 Evaluate side-chains 43 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 413 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 35 optimal weight: 0.0030 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 14 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.8162 > 50:) overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.135686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107176 restraints weight = 4037.679| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.17 r_work: 0.3061 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3323 Z= 0.128 Angle : 0.575 8.072 4534 Z= 0.289 Chirality : 0.039 0.151 543 Planarity : 0.004 0.030 550 Dihedral : 4.040 15.654 446 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.83 % Allowed : 19.83 % Favored : 77.34 % 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: 1.97 (0.41), residues: 415 helix: 2.09 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.76 (0.56), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.025 0.001 TYR A 117 PHE 0.010 0.001 PHE A 496 TRP 0.008 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 3323) covalent geometry : angle 0.57473 / 0.29 ( 4534) hydrogen bonds : bond 0.04210 / 2.69 ( 255) hydrogen bonds : angle 4.35578 / 3.04 ( 756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.071 Fit side-chains REVERT: A 126 ILE cc_start: 0.8875 (tp) cc_final: 0.8589 (tp) REVERT: A 136 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6328 (mt-10) REVERT: A 277 MET cc_start: 0.7814 (ttp) cc_final: 0.7612 (ttm) REVERT: A 388 CYS cc_start: 0.6671 (OUTLIER) cc_final: 0.5495 (m) REVERT: A 390 LEU cc_start: 0.7465 (mt) cc_final: 0.6644 (tt) REVERT: A 409 SER cc_start: 0.8961 (t) cc_final: 0.8721 (m) outliers start: 10 outliers final: 2 residues processed: 53 average time/residue: 0.5265 time to fit residues: 28.7069 Evaluate side-chains 44 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.134943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106194 restraints weight = 4116.372| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.18 r_work: 0.3041 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3323 Z= 0.134 Angle : 0.581 7.762 4534 Z= 0.292 Chirality : 0.040 0.153 543 Planarity : 0.004 0.031 550 Dihedral : 4.041 16.068 446 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.25 % Allowed : 19.83 % Favored : 75.92 % 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: 2.12 (0.41), residues: 415 helix: 2.18 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.66 (0.56), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.025 0.001 TYR A 117 PHE 0.010 0.001 PHE A 496 TRP 0.009 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 3323) covalent geometry : angle 0.58107 / 0.29 ( 4534) hydrogen bonds : bond 0.04210 / 2.69 ( 255) hydrogen bonds : angle 4.28312 / 3.00 ( 756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.114 Fit side-chains REVERT: A 126 ILE cc_start: 0.9016 (tp) cc_final: 0.8699 (tp) REVERT: A 136 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6597 (mt-10) REVERT: A 277 MET cc_start: 0.8022 (ttp) cc_final: 0.7784 (ttm) REVERT: A 323 LYS cc_start: 0.7907 (tmtp) cc_final: 0.7309 (tmmt) REVERT: A 388 CYS cc_start: 0.6626 (OUTLIER) cc_final: 0.5526 (m) REVERT: A 390 LEU cc_start: 0.7504 (mt) cc_final: 0.6701 (tt) REVERT: A 409 SER cc_start: 0.9042 (t) cc_final: 0.8809 (m) outliers start: 15 outliers final: 3 residues processed: 54 average time/residue: 0.4685 time to fit residues: 26.0963 Evaluate side-chains 48 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.135447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107115 restraints weight = 4153.602| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.18 r_work: 0.3043 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3323 Z= 0.130 Angle : 0.577 7.663 4534 Z= 0.290 Chirality : 0.040 0.152 543 Planarity : 0.004 0.031 550 Dihedral : 4.061 16.409 446 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.83 % Allowed : 22.38 % Favored : 74.79 % 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: 2.15 (0.41), residues: 415 helix: 2.20 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.62 (0.56), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 174 TYR 0.025 0.001 TYR A 117 PHE 0.010 0.001 PHE A 496 TRP 0.008 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 3323) covalent geometry : angle 0.57748 / 0.29 ( 4534) hydrogen bonds : bond 0.04101 / 2.61 ( 255) hydrogen bonds : angle 4.22476 / 2.97 ( 756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.119 Fit side-chains REVERT: A 126 ILE cc_start: 0.8948 (tp) cc_final: 0.8659 (tp) REVERT: A 136 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6512 (mt-10) REVERT: A 277 MET cc_start: 0.7952 (ttp) cc_final: 0.7723 (ttm) REVERT: A 323 LYS cc_start: 0.7970 (tmtp) cc_final: 0.7358 (tmmt) REVERT: A 388 CYS cc_start: 0.6252 (OUTLIER) cc_final: 0.5431 (m) REVERT: A 390 LEU cc_start: 0.7490 (mt) cc_final: 0.6728 (tt) REVERT: A 409 SER cc_start: 0.9006 (t) cc_final: 0.8781 (m) outliers start: 10 outliers final: 4 residues processed: 51 average time/residue: 0.5686 time to fit residues: 29.8737 Evaluate side-chains 48 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 21 optimal weight: 0.0670 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.137125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108682 restraints weight = 4129.625| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.20 r_work: 0.3097 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3323 Z= 0.120 Angle : 0.571 8.083 4534 Z= 0.285 Chirality : 0.039 0.150 543 Planarity : 0.004 0.030 550 Dihedral : 4.007 16.621 446 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.55 % Allowed : 23.23 % Favored : 74.22 % 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: 2.19 (0.41), residues: 415 helix: 2.23 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.69 (0.56), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 174 TYR 0.024 0.001 TYR A 117 PHE 0.010 0.001 PHE A 496 TRP 0.008 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 3323) covalent geometry : angle 0.57053 / 0.29 ( 4534) hydrogen bonds : bond 0.03910 / 2.49 ( 255) hydrogen bonds : angle 4.13020 / 2.91 ( 756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.118 Fit side-chains REVERT: A 126 ILE cc_start: 0.8799 (tp) cc_final: 0.8524 (tp) REVERT: A 128 TYR cc_start: 0.8470 (m-80) cc_final: 0.7856 (m-80) REVERT: A 136 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6277 (mt-10) REVERT: A 154 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8744 (mtm) REVERT: A 279 TYR cc_start: 0.6733 (t80) cc_final: 0.5579 (m-80) REVERT: A 323 LYS cc_start: 0.7838 (tmtp) cc_final: 0.7221 (tmmt) REVERT: A 388 CYS cc_start: 0.6349 (OUTLIER) cc_final: 0.5593 (m) REVERT: A 390 LEU cc_start: 0.7389 (mt) cc_final: 0.6617 (tt) REVERT: A 409 SER cc_start: 0.8899 (t) cc_final: 0.8693 (m) outliers start: 9 outliers final: 3 residues processed: 52 average time/residue: 0.5189 time to fit residues: 27.8733 Evaluate side-chains 48 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.135770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106499 restraints weight = 4151.488| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.25 r_work: 0.2984 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3323 Z= 0.134 Angle : 0.586 8.342 4534 Z= 0.294 Chirality : 0.040 0.154 543 Planarity : 0.004 0.031 550 Dihedral : 4.055 16.810 446 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.55 % Allowed : 22.66 % Favored : 74.79 % 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: 2.16 (0.42), residues: 415 helix: 2.19 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.66 (0.56), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 174 TYR 0.025 0.001 TYR A 117 PHE 0.009 0.001 PHE A 496 TRP 0.008 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 3323) covalent geometry : angle 0.58630 / 0.29 ( 4534) hydrogen bonds : bond 0.04042 / 2.58 ( 255) hydrogen bonds : angle 4.15450 / 2.93 ( 756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.119 Fit side-chains REVERT: A 126 ILE cc_start: 0.8718 (tp) cc_final: 0.8434 (tp) REVERT: A 136 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6219 (mt-10) REVERT: A 154 MET cc_start: 0.8988 (mtm) cc_final: 0.8664 (mtm) REVERT: A 279 TYR cc_start: 0.6599 (t80) cc_final: 0.5464 (m-80) REVERT: A 323 LYS cc_start: 0.7661 (tmtp) cc_final: 0.7060 (tmmt) REVERT: A 388 CYS cc_start: 0.6292 (OUTLIER) cc_final: 0.5575 (m) REVERT: A 409 SER cc_start: 0.8901 (t) cc_final: 0.8676 (m) outliers start: 9 outliers final: 3 residues processed: 49 average time/residue: 0.5462 time to fit residues: 27.6194 Evaluate side-chains 45 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.136915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107641 restraints weight = 4142.817| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.24 r_work: 0.3062 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3323 Z= 0.123 Angle : 0.580 8.075 4534 Z= 0.290 Chirality : 0.039 0.153 543 Planarity : 0.004 0.032 550 Dihedral : 4.020 16.106 446 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.98 % Allowed : 23.23 % Favored : 74.79 % 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: 2.26 (0.41), residues: 415 helix: 2.26 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.62 (0.56), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 174 TYR 0.024 0.001 TYR A 117 PHE 0.009 0.001 PHE A 496 TRP 0.008 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 3323) covalent geometry : angle 0.57958 / 0.29 ( 4534) hydrogen bonds : bond 0.03940 / 2.51 ( 255) hydrogen bonds : angle 4.10285 / 2.90 ( 756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.115 Fit side-chains REVERT: A 126 ILE cc_start: 0.9017 (tp) cc_final: 0.8736 (tp) REVERT: A 136 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6681 (mt-10) REVERT: A 154 MET cc_start: 0.9238 (mtm) cc_final: 0.8980 (mtm) REVERT: A 279 TYR cc_start: 0.7041 (t80) cc_final: 0.5887 (m-80) REVERT: A 323 LYS cc_start: 0.8012 (tmtp) cc_final: 0.7399 (tmmt) REVERT: A 388 CYS cc_start: 0.6402 (OUTLIER) cc_final: 0.5752 (m) outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 0.5007 time to fit residues: 25.2871 Evaluate side-chains 44 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 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 = 0.3577 r_free = 0.3577 target = 0.136941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108680 restraints weight = 4100.703| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.14 r_work: 0.3108 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3323 Z= 0.126 Angle : 0.585 7.987 4534 Z= 0.293 Chirality : 0.039 0.153 543 Planarity : 0.004 0.033 550 Dihedral : 4.030 15.904 446 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.27 % Allowed : 23.23 % Favored : 74.50 % 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: 2.23 (0.41), residues: 415 helix: 2.20 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.50 (0.56), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 174 TYR 0.024 0.001 TYR A 117 PHE 0.010 0.001 PHE A 496 TRP 0.009 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 3323) covalent geometry : angle 0.58534 / 0.29 ( 4534) hydrogen bonds : bond 0.03943 / 2.51 ( 255) hydrogen bonds : angle 4.10303 / 2.90 ( 756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.078 Fit side-chains REVERT: A 126 ILE cc_start: 0.8854 (tp) cc_final: 0.8581 (tp) REVERT: A 136 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6399 (mt-10) REVERT: A 154 MET cc_start: 0.9126 (mtm) cc_final: 0.8810 (mtm) REVERT: A 279 TYR cc_start: 0.6801 (t80) cc_final: 0.5646 (m-80) REVERT: A 323 LYS cc_start: 0.7830 (tmtp) cc_final: 0.7226 (tmmt) REVERT: A 388 CYS cc_start: 0.6384 (OUTLIER) cc_final: 0.5806 (m) REVERT: A 512 LYS cc_start: 0.7526 (pttp) cc_final: 0.7323 (pttp) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 0.3747 time to fit residues: 18.5387 Evaluate side-chains 48 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.136353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107864 restraints weight = 4118.122| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.15 r_work: 0.3076 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3323 Z= 0.135 Angle : 0.602 9.098 4534 Z= 0.301 Chirality : 0.040 0.155 543 Planarity : 0.004 0.033 550 Dihedral : 4.056 15.865 446 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.98 % Allowed : 23.80 % Favored : 74.22 % 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: 2.25 (0.41), residues: 415 helix: 2.22 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.44 (0.55), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 174 TYR 0.024 0.001 TYR A 117 PHE 0.010 0.001 PHE A 496 TRP 0.009 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 3323) covalent geometry : angle 0.60215 / 0.30 ( 4534) hydrogen bonds : bond 0.04039 / 2.58 ( 255) hydrogen bonds : angle 4.12161 / 2.91 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1118.94 seconds wall clock time: 19 minutes 49.02 seconds (1189.02 seconds total)