Starting phenix.real_space_refine on Tue Mar 3 12:39:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hfl_34722/03_2026/8hfl_34722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfl_34722/03_2026/8hfl_34722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hfl_34722/03_2026/8hfl_34722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfl_34722/03_2026/8hfl_34722.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hfl_34722/03_2026/8hfl_34722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfl_34722/03_2026/8hfl_34722.map" } resolution = 3.0 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= 0.002 sd= 0.140 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 S 20 5.16 5 Cl 2 4.86 5 C 2980 2.51 5 N 689 2.21 5 O 750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4441 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4421 Classifications: {'peptide': 553} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 533} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 20 Unusual residues: {' CL': 1, '1XR': 1} Classifications: {'undetermined': 2, 'water': 3} Link IDs: {None: 4} Time building chain proxies: 1.06, per 1000 atoms: 0.24 Number of scatterers: 4441 At special positions: 0 Unit cell: (68.1975, 71.445, 98.5075, 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) Cl 2 17.00 S 20 16.00 O 750 8.00 N 689 7.00 C 2980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 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: 0.39 Conformation dependent library (CDL) restraints added in 348.4 milliseconds 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1016 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 1 sheets defined 80.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.515A pdb=" N VAL A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 removed outlier: 4.367A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.629A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 148 Processing helix chain 'A' and resid 151 through 166 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 removed outlier: 3.590A pdb=" N LEU A 239 " --> pdb=" O TRP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 264 through 283 Proline residue: A 270 - end of helix removed outlier: 4.106A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.744A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Proline residue: A 392 - end of helix removed outlier: 3.700A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.758A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 removed outlier: 3.523A pdb=" N LYS A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.719A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 496 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.554A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.774A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 292 hydrogen bonds defined for protein. 849 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: 0.60 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1297 1.34 - 1.46: 974 1.46 - 1.58: 2277 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 4580 Sorted by residual: bond pdb=" N GLY A 60 " pdb=" CA GLY A 60 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.95e+00 bond pdb=" C2 1XR A 701 " pdb=" N1 1XR A 701 " ideal model delta sigma weight residual 1.441 1.477 -0.036 2.00e-02 2.50e+03 3.17e+00 bond pdb=" C10 1XR A 701 " pdb=" N1 1XR A 701 " ideal model delta sigma weight residual 1.467 1.490 -0.023 2.00e-02 2.50e+03 1.30e+00 bond pdb=" CA LEU A 102 " pdb=" C LEU A 102 " ideal model delta sigma weight residual 1.524 1.511 0.013 1.28e-02 6.10e+03 1.09e+00 bond pdb=" C1 1XR A 701 " pdb=" C2 1XR A 701 " ideal model delta sigma weight residual 1.542 1.522 0.020 2.00e-02 2.50e+03 9.88e-01 ... (remaining 4575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 6100 1.50 - 3.00: 111 3.00 - 4.50: 32 4.50 - 6.00: 4 6.00 - 7.50: 1 Bond angle restraints: 6248 Sorted by residual: angle pdb=" C GLY A 106 " pdb=" N MET A 107 " pdb=" CA MET A 107 " ideal model delta sigma weight residual 119.78 116.12 3.66 1.24e+00 6.50e-01 8.70e+00 angle pdb=" N VAL A 263 " pdb=" CA VAL A 263 " pdb=" C VAL A 263 " ideal model delta sigma weight residual 113.00 109.26 3.74 1.30e+00 5.92e-01 8.26e+00 angle pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" C TYR A 205 " ideal model delta sigma weight residual 110.80 116.58 -5.78 2.13e+00 2.20e-01 7.36e+00 angle pdb=" C1 1XR A 701 " pdb=" C2 1XR A 701 " pdb=" N1 1XR A 701 " ideal model delta sigma weight residual 117.04 109.54 7.50 3.00e+00 1.11e-01 6.25e+00 angle pdb=" CA MET A 107 " pdb=" C MET A 107 " pdb=" N PRO A 108 " ideal model delta sigma weight residual 120.81 118.72 2.09 8.60e-01 1.35e+00 5.88e+00 ... (remaining 6243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 2237 16.52 - 33.04: 241 33.04 - 49.56: 62 49.56 - 66.08: 23 66.08 - 82.60: 2 Dihedral angle restraints: 2565 sinusoidal: 968 harmonic: 1597 Sorted by residual: dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual -180.00 -157.01 -22.99 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -133.33 10.73 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual 122.80 132.57 -9.77 0 2.50e+00 1.60e-01 1.53e+01 ... (remaining 2562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 666 0.088 - 0.176: 28 0.176 - 0.264: 0 0.264 - 0.351: 0 0.351 - 0.439: 2 Chirality restraints: 696 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CA HIS A 372 " pdb=" N HIS A 372 " pdb=" C HIS A 372 " pdb=" CB HIS A 372 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C2 1XR A 701 " pdb=" C1 1XR A 701 " pdb=" C3 1XR A 701 " pdb=" N1 1XR A 701 " both_signs ideal model delta sigma weight residual False -2.43 -2.59 0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 693 not shown) Planarity restraints: 759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C ILE A 103 " -0.063 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 492 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C VAL A 492 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A 492 " 0.015 2.00e-02 2.50e+03 pdb=" N SER A 493 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 102 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C LEU A 102 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU A 102 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE A 103 " 0.012 2.00e-02 2.50e+03 ... (remaining 756 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 26 2.56 - 3.15: 3663 3.15 - 3.73: 6973 3.73 - 4.32: 9679 4.32 - 4.90: 16767 Nonbonded interactions: 37108 Sorted by model distance: nonbonded pdb=" OD1 ASP A 75 " pdb=" OG SER A 419 " model vdw 1.981 3.040 nonbonded pdb=" OG1 THR A 479 " pdb=" OG SER A 536 " model vdw 2.179 3.040 nonbonded pdb=" NZ LYS A 189 " pdb=" OE2 GLU A 371 " model vdw 2.195 3.120 nonbonded pdb=" O ALA A 328 " pdb=" OG SER A 331 " model vdw 2.236 3.040 nonbonded pdb=" O THR A 283 " pdb=" OG1 THR A 283 " model vdw 2.303 3.040 ... (remaining 37103 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: 0.640 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.890 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:10.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 0.039 4581 Z= 0.136 Angle : 0.548 7.502 6250 Z= 0.296 Chirality : 0.044 0.439 696 Planarity : 0.004 0.037 759 Dihedral : 15.471 82.598 1546 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.73 % Favored : 97.09 % Rotamer: Outliers : 1.72 % Allowed : 17.17 % Favored : 81.12 % Cbeta Deviations : 0.20 % 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: 1.46 (0.37), residues: 549 helix: 1.52 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.10 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 607 TYR 0.014 0.001 TYR A 590 PHE 0.013 0.001 PHE A 403 TRP 0.007 0.001 TRP A 553 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4580) covalent geometry : angle 0.54792 ( 6248) SS BOND : bond 0.00009 ( 1) SS BOND : angle 1.44771 ( 2) hydrogen bonds : bond 0.13950 ( 292) hydrogen bonds : angle 5.43652 ( 849) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.166 Fit side-chains REVERT: A 509 MET cc_start: 0.8974 (mtp) cc_final: 0.8716 (mtt) REVERT: A 606 ILE cc_start: 0.8229 (mm) cc_final: 0.8016 (mm) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.2735 time to fit residues: 15.0311 Evaluate side-chains 48 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 536 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.095342 restraints weight = 5216.298| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.81 r_work: 0.2903 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4581 Z= 0.129 Angle : 0.513 6.770 6250 Z= 0.266 Chirality : 0.040 0.173 696 Planarity : 0.004 0.034 759 Dihedral : 6.029 48.592 615 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.37 % Favored : 97.45 % Rotamer: Outliers : 2.79 % Allowed : 14.81 % Favored : 82.40 % 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: 1.40 (0.37), residues: 549 helix: 1.36 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.01 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.017 0.001 TYR A 590 PHE 0.015 0.001 PHE A 110 TRP 0.009 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4580) covalent geometry : angle 0.51253 ( 6248) SS BOND : bond 0.00118 ( 1) SS BOND : angle 1.58320 ( 2) hydrogen bonds : bond 0.04561 ( 292) hydrogen bonds : angle 4.68579 ( 849) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.119 Fit side-chains REVERT: A 271 TYR cc_start: 0.8414 (m-80) cc_final: 0.7981 (m-80) REVERT: A 377 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: A 421 MET cc_start: 0.7790 (mtp) cc_final: 0.7546 (mtm) REVERT: A 434 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8707 (m-30) REVERT: A 509 MET cc_start: 0.8946 (mtp) cc_final: 0.8664 (mtt) REVERT: A 606 ILE cc_start: 0.8035 (mm) cc_final: 0.7783 (mm) outliers start: 13 outliers final: 3 residues processed: 63 average time/residue: 0.2813 time to fit residues: 18.9982 Evaluate side-chains 51 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 434 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 16 optimal weight: 0.0980 chunk 46 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.0030 chunk 41 optimal weight: 0.0040 chunk 12 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 overall best weight: 0.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.127035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.100406 restraints weight = 5173.815| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.73 r_work: 0.2959 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 4581 Z= 0.106 Angle : 0.483 6.677 6250 Z= 0.248 Chirality : 0.039 0.136 696 Planarity : 0.004 0.030 759 Dihedral : 5.210 35.154 608 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.55 % Favored : 97.27 % Rotamer: Outliers : 1.93 % Allowed : 17.81 % Favored : 80.26 % 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: 1.47 (0.37), residues: 549 helix: 1.49 (0.27), residues: 393 sheet: None (None), residues: 0 loop : -0.22 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.014 0.001 TYR A 84 PHE 0.013 0.001 PHE A 110 TRP 0.010 0.001 TRP A 553 HIS 0.002 0.000 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 4580) covalent geometry : angle 0.48243 ( 6248) SS BOND : bond 0.00257 ( 1) SS BOND : angle 1.52805 ( 2) hydrogen bonds : bond 0.03921 ( 292) hydrogen bonds : angle 4.47238 ( 849) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.145 Fit side-chains REVERT: A 271 TYR cc_start: 0.8233 (m-80) cc_final: 0.7873 (m-80) REVERT: A 376 ILE cc_start: 0.7146 (mp) cc_final: 0.6833 (mp) REVERT: A 377 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: A 399 SER cc_start: 0.7986 (t) cc_final: 0.7776 (m) REVERT: A 434 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8617 (m-30) REVERT: A 509 MET cc_start: 0.8813 (mtp) cc_final: 0.8580 (mtt) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 0.2132 time to fit residues: 13.9646 Evaluate side-chains 55 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.105238 restraints weight = 5119.610| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.71 r_work: 0.2894 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4581 Z= 0.129 Angle : 0.494 6.735 6250 Z= 0.255 Chirality : 0.040 0.135 696 Planarity : 0.004 0.030 759 Dihedral : 5.273 35.882 608 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.73 % Favored : 97.09 % Rotamer: Outliers : 2.79 % Allowed : 17.81 % Favored : 79.40 % 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: 1.49 (0.37), residues: 549 helix: 1.51 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.21 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 442 TYR 0.017 0.001 TYR A 84 PHE 0.013 0.001 PHE A 110 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4580) covalent geometry : angle 0.49355 ( 6248) SS BOND : bond 0.00159 ( 1) SS BOND : angle 1.66253 ( 2) hydrogen bonds : bond 0.04377 ( 292) hydrogen bonds : angle 4.55943 ( 849) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.194 Fit side-chains REVERT: A 271 TYR cc_start: 0.8285 (m-80) cc_final: 0.7895 (m-80) REVERT: A 376 ILE cc_start: 0.7153 (mp) cc_final: 0.6796 (mp) REVERT: A 377 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: A 399 SER cc_start: 0.8292 (t) cc_final: 0.8061 (m) REVERT: A 420 SER cc_start: 0.8756 (OUTLIER) cc_final: 0.8173 (m) REVERT: A 434 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8633 (m-30) REVERT: A 587 ARG cc_start: 0.8522 (mtt90) cc_final: 0.8061 (mmt90) REVERT: A 606 ILE cc_start: 0.8092 (mm) cc_final: 0.7846 (mm) outliers start: 13 outliers final: 4 residues processed: 62 average time/residue: 0.2223 time to fit residues: 14.9840 Evaluate side-chains 59 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.123602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.096308 restraints weight = 5192.940| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.74 r_work: 0.2922 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4581 Z= 0.138 Angle : 0.500 6.559 6250 Z= 0.259 Chirality : 0.040 0.130 696 Planarity : 0.004 0.030 759 Dihedral : 5.283 35.402 608 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.22 % Allowed : 18.24 % Favored : 78.54 % 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: 1.42 (0.37), residues: 549 helix: 1.47 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.29 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 442 TYR 0.019 0.001 TYR A 84 PHE 0.013 0.001 PHE A 110 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4580) covalent geometry : angle 0.49934 ( 6248) SS BOND : bond 0.00179 ( 1) SS BOND : angle 1.71856 ( 2) hydrogen bonds : bond 0.04477 ( 292) hydrogen bonds : angle 4.57115 ( 849) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.146 Fit side-chains REVERT: A 271 TYR cc_start: 0.8383 (m-80) cc_final: 0.7939 (m-80) REVERT: A 376 ILE cc_start: 0.7224 (mp) cc_final: 0.6820 (mp) REVERT: A 377 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8220 (mp0) REVERT: A 399 SER cc_start: 0.8304 (t) cc_final: 0.8036 (m) REVERT: A 420 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8250 (m) REVERT: A 434 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8666 (m-30) REVERT: A 587 ARG cc_start: 0.8466 (mtt90) cc_final: 0.7967 (mmt90) outliers start: 15 outliers final: 5 residues processed: 63 average time/residue: 0.2764 time to fit residues: 18.8343 Evaluate side-chains 57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 53 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.124872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.097053 restraints weight = 5325.743| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.80 r_work: 0.2902 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4581 Z= 0.114 Angle : 0.491 6.556 6250 Z= 0.252 Chirality : 0.039 0.136 696 Planarity : 0.004 0.029 759 Dihedral : 5.216 35.727 608 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.00 % Allowed : 19.10 % Favored : 77.90 % 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: 1.53 (0.37), residues: 549 helix: 1.58 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -0.33 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 341 TYR 0.017 0.001 TYR A 84 PHE 0.011 0.001 PHE A 110 TRP 0.009 0.001 TRP A 553 HIS 0.002 0.000 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 4580) covalent geometry : angle 0.49036 ( 6248) SS BOND : bond 0.00089 ( 1) SS BOND : angle 1.58830 ( 2) hydrogen bonds : bond 0.04063 ( 292) hydrogen bonds : angle 4.47949 ( 849) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.145 Fit side-chains REVERT: A 271 TYR cc_start: 0.8216 (m-80) cc_final: 0.7830 (m-80) REVERT: A 376 ILE cc_start: 0.7100 (mp) cc_final: 0.6834 (mp) REVERT: A 377 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: A 399 SER cc_start: 0.8172 (t) cc_final: 0.7909 (m) REVERT: A 420 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8275 (m) REVERT: A 434 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8541 (m-30) REVERT: A 459 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.7103 (t80) REVERT: A 590 TYR cc_start: 0.8114 (m-80) cc_final: 0.7883 (m-80) REVERT: A 606 ILE cc_start: 0.8163 (mm) cc_final: 0.7872 (mp) outliers start: 14 outliers final: 4 residues processed: 61 average time/residue: 0.2700 time to fit residues: 17.5844 Evaluate side-chains 56 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 32 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.122985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.095170 restraints weight = 5298.097| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.77 r_work: 0.2878 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4581 Z= 0.134 Angle : 0.510 6.673 6250 Z= 0.261 Chirality : 0.040 0.138 696 Planarity : 0.004 0.029 759 Dihedral : 5.235 35.261 608 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.36 % Allowed : 19.10 % Favored : 78.54 % 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: 1.45 (0.37), residues: 549 helix: 1.51 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -0.33 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 341 TYR 0.019 0.001 TYR A 84 PHE 0.012 0.001 PHE A 94 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4580) covalent geometry : angle 0.50864 ( 6248) SS BOND : bond 0.00053 ( 1) SS BOND : angle 1.82621 ( 2) hydrogen bonds : bond 0.04412 ( 292) hydrogen bonds : angle 4.54272 ( 849) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.161 Fit side-chains REVERT: A 271 TYR cc_start: 0.8345 (m-80) cc_final: 0.7948 (m-80) REVERT: A 377 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: A 399 SER cc_start: 0.8435 (t) cc_final: 0.8166 (m) REVERT: A 420 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8234 (m) REVERT: A 434 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8556 (m-30) REVERT: A 606 ILE cc_start: 0.8190 (mm) cc_final: 0.7933 (mp) outliers start: 11 outliers final: 5 residues processed: 58 average time/residue: 0.2326 time to fit residues: 14.6170 Evaluate side-chains 56 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 0.0040 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.126653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.099560 restraints weight = 5174.656| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.74 r_work: 0.2942 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 4581 Z= 0.110 Angle : 0.491 8.127 6250 Z= 0.250 Chirality : 0.039 0.139 696 Planarity : 0.004 0.028 759 Dihedral : 5.141 35.689 608 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.58 % Allowed : 19.10 % Favored : 78.33 % 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: 1.57 (0.37), residues: 549 helix: 1.60 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -0.29 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 121 TYR 0.016 0.001 TYR A 84 PHE 0.010 0.001 PHE A 362 TRP 0.009 0.001 TRP A 553 HIS 0.001 0.000 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 4580) covalent geometry : angle 0.49035 ( 6248) SS BOND : bond 0.00072 ( 1) SS BOND : angle 1.51829 ( 2) hydrogen bonds : bond 0.03966 ( 292) hydrogen bonds : angle 4.44631 ( 849) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.217 Fit side-chains REVERT: A 271 TYR cc_start: 0.8297 (m-80) cc_final: 0.7912 (m-80) REVERT: A 376 ILE cc_start: 0.7305 (mp) cc_final: 0.6992 (mp) REVERT: A 377 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8336 (mp0) REVERT: A 399 SER cc_start: 0.8365 (t) cc_final: 0.8103 (m) REVERT: A 420 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.8297 (m) REVERT: A 434 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8479 (m-30) REVERT: A 459 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.7121 (t80) REVERT: A 590 TYR cc_start: 0.8194 (m-80) cc_final: 0.7987 (m-80) REVERT: A 606 ILE cc_start: 0.8208 (mm) cc_final: 0.7951 (mp) outliers start: 12 outliers final: 5 residues processed: 59 average time/residue: 0.2338 time to fit residues: 15.0960 Evaluate side-chains 57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 37 optimal weight: 0.0770 chunk 54 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.0270 chunk 19 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.125616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.097832 restraints weight = 5222.714| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.78 r_work: 0.2938 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4581 Z= 0.111 Angle : 0.481 6.440 6250 Z= 0.246 Chirality : 0.039 0.145 696 Planarity : 0.004 0.028 759 Dihedral : 5.111 35.345 608 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.36 % Allowed : 20.17 % Favored : 77.47 % 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: 1.60 (0.37), residues: 549 helix: 1.63 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -0.28 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 121 TYR 0.016 0.001 TYR A 84 PHE 0.010 0.001 PHE A 110 TRP 0.009 0.001 TRP A 553 HIS 0.001 0.000 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 4580) covalent geometry : angle 0.47985 ( 6248) SS BOND : bond 0.00061 ( 1) SS BOND : angle 1.53973 ( 2) hydrogen bonds : bond 0.04025 ( 292) hydrogen bonds : angle 4.43267 ( 849) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.171 Fit side-chains REVERT: A 271 TYR cc_start: 0.8243 (m-80) cc_final: 0.7911 (m-80) REVERT: A 376 ILE cc_start: 0.7275 (mp) cc_final: 0.6992 (mp) REVERT: A 377 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8316 (mp0) REVERT: A 399 SER cc_start: 0.8352 (t) cc_final: 0.8096 (m) REVERT: A 420 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8238 (m) REVERT: A 434 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8446 (m-30) REVERT: A 459 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.7113 (t80) REVERT: A 507 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: A 606 ILE cc_start: 0.8177 (mm) cc_final: 0.7944 (mp) outliers start: 11 outliers final: 5 residues processed: 57 average time/residue: 0.2373 time to fit residues: 14.6550 Evaluate side-chains 57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 507 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.0470 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.125194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.097553 restraints weight = 5204.756| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.78 r_work: 0.2916 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4581 Z= 0.131 Angle : 0.506 7.670 6250 Z= 0.258 Chirality : 0.040 0.143 696 Planarity : 0.004 0.028 759 Dihedral : 5.111 34.844 608 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.36 % Allowed : 20.17 % Favored : 77.47 % 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: 1.53 (0.37), residues: 549 helix: 1.59 (0.27), residues: 390 sheet: None (None), residues: 0 loop : -0.32 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 341 TYR 0.018 0.001 TYR A 84 PHE 0.014 0.001 PHE A 408 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 4580) covalent geometry : angle 0.50497 ( 6248) SS BOND : bond 0.00059 ( 1) SS BOND : angle 1.70355 ( 2) hydrogen bonds : bond 0.04266 ( 292) hydrogen bonds : angle 4.50667 ( 849) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.116 Fit side-chains REVERT: A 271 TYR cc_start: 0.8302 (m-80) cc_final: 0.7953 (m-80) REVERT: A 304 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7072 (mm-30) REVERT: A 399 SER cc_start: 0.8395 (t) cc_final: 0.8131 (m) REVERT: A 420 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8192 (m) REVERT: A 434 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8458 (m-30) REVERT: A 507 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: A 606 ILE cc_start: 0.8184 (mm) cc_final: 0.7970 (mp) outliers start: 11 outliers final: 5 residues processed: 60 average time/residue: 0.2458 time to fit residues: 15.9180 Evaluate side-chains 59 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 507 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 6 optimal weight: 0.0040 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.126220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.098979 restraints weight = 5192.244| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.76 r_work: 0.2933 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4581 Z= 0.119 Angle : 0.499 6.931 6250 Z= 0.255 Chirality : 0.039 0.142 696 Planarity : 0.004 0.028 759 Dihedral : 5.135 35.046 608 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.15 % Allowed : 20.17 % Favored : 77.68 % 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: 1.58 (0.37), residues: 549 helix: 1.62 (0.27), residues: 390 sheet: None (None), residues: 0 loop : -0.32 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 341 TYR 0.017 0.001 TYR A 84 PHE 0.014 0.001 PHE A 408 TRP 0.012 0.001 TRP A 264 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4580) covalent geometry : angle 0.49818 ( 6248) SS BOND : bond 0.00071 ( 1) SS BOND : angle 1.56887 ( 2) hydrogen bonds : bond 0.04100 ( 292) hydrogen bonds : angle 4.48561 ( 849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1297.92 seconds wall clock time: 22 minutes 51.95 seconds (1371.95 seconds total)