Starting phenix.real_space_refine on Wed Jul 1 23:58:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hfl_34722/07_2026/8hfl_34722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfl_34722/07_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_34722/07_2026/8hfl_34722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfl_34722/07_2026/8hfl_34722.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hfl_34722/07_2026/8hfl_34722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfl_34722/07_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-6108/lib/python3.11/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, 19 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'1XR': 1} Classifications: {'undetermined': 1, 'water': 3} Link IDs: {None: 2} Chain breaks: 1 Time building chain proxies: 0.89, per 1000 atoms: 0.20 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: 0.41 Conformation dependent library (CDL) restraints added in 164.0 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: 0.14 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: 0.73 Time building geometry restraints manager: 0.55 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: 0.590 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.580 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:8.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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/Z covalent geometry : bond 0.00287 / 0.14 ( 4580) covalent geometry : angle 0.54792 / 0.30 ( 6248) SS BOND : bond 0.00009 / 0.01 ( 1) SS BOND : angle 1.44771 / 0.56 ( 2) hydrogen bonds : bond 0.13950 / 8.53 ( 292) hydrogen bonds : angle 5.43652 / 3.86 ( 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 : 0.101 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: 0.2228 time to fit residues: 12.3022 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 : 0.106 ------------------------------------------------------------------------------- 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: 0.7980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.096322 restraints weight = 5196.133| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.82 r_work: 0.2877 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4581 Z= 0.134 Angle : 0.517 6.581 6250 Z= 0.268 Chirality : 0.040 0.172 696 Planarity : 0.004 0.034 759 Dihedral : 6.025 48.589 615 Min Nonbonded Distance : 2.529 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 : 0.00 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.016 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/Z covalent geometry : bond 0.00318 / 0.13 ( 4580) covalent geometry : angle 0.51614 / 0.27 ( 6248) SS BOND : bond 0.00104 / 0.07 ( 1) SS BOND : angle 1.62259 / 0.64 ( 2) hydrogen bonds : bond 0.04632 / 3.00 ( 292) hydrogen bonds : angle 4.69996 / 3.31 ( 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 65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.098 Fit side-chains REVERT: A 377 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8101 (mp0) REVERT: A 434 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8753 (m-30) REVERT: A 509 MET cc_start: 0.8946 (mtp) cc_final: 0.8664 (mtt) REVERT: A 606 ILE cc_start: 0.8034 (mm) cc_final: 0.7777 (mm) outliers start: 13 outliers final: 3 residues processed: 61 average time/residue: 0.2169 time to fit residues: 14.2303 Evaluate side-chains 50 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.103 ------------------------------------------------------------------------------- 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: 0.0770 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 41 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.110183 restraints weight = 5111.261| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.72 r_work: 0.2966 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4581 Z= 0.101 Angle : 0.473 6.610 6250 Z= 0.243 Chirality : 0.038 0.148 696 Planarity : 0.004 0.031 759 Dihedral : 5.133 34.550 608 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.63 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: 1.56 (0.37), residues: 549 helix: 1.53 (0.27), residues: 393 sheet: None (None), residues: 0 loop : -0.11 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.013 0.001 TYR A 84 PHE 0.012 0.001 PHE A 110 TRP 0.010 0.001 TRP A 553 HIS 0.001 0.000 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 4580) covalent geometry : angle 0.47243 / 0.24 ( 6248) SS BOND : bond 0.00112 / 0.07 ( 1) SS BOND : angle 1.11410 / 0.46 ( 2) hydrogen bonds : bond 0.03741 / 2.48 ( 292) hydrogen bonds : angle 4.42933 / 3.09 ( 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 : 0.125 Fit side-chains REVERT: A 271 TYR cc_start: 0.8130 (m-80) cc_final: 0.7786 (m-80) REVERT: A 376 ILE cc_start: 0.7113 (mp) cc_final: 0.6874 (mp) REVERT: A 377 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: A 420 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8223 (m) REVERT: A 509 MET cc_start: 0.8791 (mtp) cc_final: 0.8554 (mtt) outliers start: 9 outliers final: 3 residues processed: 60 average time/residue: 0.1886 time to fit residues: 12.4932 Evaluate side-chains 53 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 377 GLU Chi-restraints excluded: chain A residue 420 SER 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: 0.9980 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.0570 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.125875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.098922 restraints weight = 5152.103| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.74 r_work: 0.2916 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1461 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= 0.130 Angle : 0.494 6.730 6250 Z= 0.255 Chirality : 0.040 0.135 696 Planarity : 0.004 0.030 759 Dihedral : 5.249 36.024 608 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.73 % Favored : 97.09 % Rotamer: Outliers : 2.79 % Allowed : 18.24 % Favored : 78.97 % 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: 1.55 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.12 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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/Z covalent geometry : bond 0.00310 / 0.13 ( 4580) covalent geometry : angle 0.49310 / 0.26 ( 6248) SS BOND : bond 0.00294 / 0.18 ( 1) SS BOND : angle 1.88685 / 0.76 ( 2) hydrogen bonds : bond 0.04375 / 2.88 ( 292) hydrogen bonds : angle 4.54428 / 3.19 ( 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 : 0.097 Fit side-chains REVERT: A 271 TYR cc_start: 0.8255 (m-80) cc_final: 0.7865 (m-80) REVERT: A 376 ILE cc_start: 0.7118 (mp) cc_final: 0.6781 (mp) REVERT: A 377 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: A 420 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8213 (m) REVERT: A 434 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8660 (m-30) REVERT: A 587 ARG cc_start: 0.8480 (mtt90) cc_final: 0.8000 (mmt90) REVERT: A 606 ILE cc_start: 0.8076 (mm) cc_final: 0.7827 (mm) outliers start: 13 outliers final: 5 residues processed: 62 average time/residue: 0.2304 time to fit residues: 15.4253 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 : 0.177 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.130659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104127 restraints weight = 5144.131| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.74 r_work: 0.2866 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1567 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= 0.136 Angle : 0.495 6.571 6250 Z= 0.257 Chirality : 0.040 0.131 696 Planarity : 0.004 0.030 759 Dihedral : 5.267 35.328 608 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.65 % Allowed : 18.03 % 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: 1.47 (0.37), residues: 549 helix: 1.50 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.25 (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/Z covalent geometry : bond 0.00328 / 0.14 ( 4580) covalent geometry : angle 0.49440 / 0.26 ( 6248) SS BOND : bond 0.00194 / 0.12 ( 1) SS BOND : angle 1.75071 / 0.69 ( 2) hydrogen bonds : bond 0.04446 / 2.93 ( 292) hydrogen bonds : angle 4.54714 / 3.20 ( 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: 17 poor density : 49 time to evaluate : 0.158 Fit side-chains REVERT: A 271 TYR cc_start: 0.8319 (m-80) cc_final: 0.7865 (m-80) REVERT: A 376 ILE cc_start: 0.7122 (mp) cc_final: 0.6756 (mp) REVERT: A 377 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8159 (mp0) REVERT: A 420 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8226 (m) REVERT: A 434 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8715 (m-30) REVERT: A 459 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.7326 (m-80) REVERT: A 587 ARG cc_start: 0.8443 (mtt90) cc_final: 0.8198 (mmt90) REVERT: A 590 TYR cc_start: 0.8115 (m-80) cc_final: 0.7890 (m-80) outliers start: 17 outliers final: 5 residues processed: 61 average time/residue: 0.2444 time to fit residues: 16.1104 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 : 0.167 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 53 optimal weight: 0.0770 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.125484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.097795 restraints weight = 5345.190| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.79 r_work: 0.2917 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 4581 Z= 0.108 Angle : 0.481 6.565 6250 Z= 0.247 Chirality : 0.039 0.139 696 Planarity : 0.004 0.029 759 Dihedral : 5.174 35.584 608 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.22 % Allowed : 19.10 % 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: 1.64 (0.37), residues: 549 helix: 1.64 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.24 (0.50), residues: 157 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 0.011 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/Z covalent geometry : bond 0.00246 / 0.11 ( 4580) covalent geometry : angle 0.48016 / 0.25 ( 6248) SS BOND : bond 0.00121 / 0.08 ( 1) SS BOND : angle 1.49992 / 0.57 ( 2) hydrogen bonds : bond 0.03917 / 2.60 ( 292) hydrogen bonds : angle 4.43199 / 3.11 ( 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 64 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.142 Fit side-chains REVERT: A 271 TYR cc_start: 0.8198 (m-80) cc_final: 0.7814 (m-80) REVERT: A 376 ILE cc_start: 0.7102 (mp) cc_final: 0.6866 (mp) REVERT: A 420 SER cc_start: 0.8703 (OUTLIER) cc_final: 0.8274 (m) REVERT: A 434 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8602 (m-30) REVERT: A 587 ARG cc_start: 0.8438 (mtt90) cc_final: 0.7926 (mmt90) REVERT: A 590 TYR cc_start: 0.8208 (m-80) cc_final: 0.7989 (m-80) REVERT: A 606 ILE cc_start: 0.8169 (mm) cc_final: 0.7873 (mp) outliers start: 15 outliers final: 5 residues processed: 60 average time/residue: 0.2384 time to fit residues: 15.5317 Evaluate side-chains 55 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.124604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.097218 restraints weight = 5237.987| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.75 r_work: 0.2910 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1706 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= 0.132 Angle : 0.499 6.657 6250 Z= 0.256 Chirality : 0.040 0.138 696 Planarity : 0.004 0.029 759 Dihedral : 5.197 35.064 608 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.22 % Allowed : 18.88 % 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: 1.56 (0.37), residues: 549 helix: 1.59 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.30 (0.50), residues: 157 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 0.012 0.001 PHE A 409 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 4580) covalent geometry : angle 0.49757 / 0.26 ( 6248) SS BOND : bond 0.00036 / 0.02 ( 1) SS BOND : angle 1.79163 / 0.68 ( 2) hydrogen bonds : bond 0.04317 / 2.85 ( 292) hydrogen bonds : angle 4.51179 / 3.17 ( 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 64 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.123 Fit side-chains REVERT: A 271 TYR cc_start: 0.8335 (m-80) cc_final: 0.8002 (m-80) REVERT: A 420 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8242 (m) REVERT: A 434 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8653 (m-30) REVERT: A 459 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7180 (m-80) REVERT: A 590 TYR cc_start: 0.8298 (m-80) cc_final: 0.7531 (m-80) REVERT: A 606 ILE cc_start: 0.8222 (mm) cc_final: 0.7964 (mp) outliers start: 15 outliers final: 7 residues processed: 59 average time/residue: 0.2357 time to fit residues: 15.0467 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 : 0.116 ------------------------------------------------------------------------------- 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 336 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.0770 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.125388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.098212 restraints weight = 5178.857| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.74 r_work: 0.2926 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4581 Z= 0.118 Angle : 0.486 6.456 6250 Z= 0.250 Chirality : 0.039 0.140 696 Planarity : 0.004 0.028 759 Dihedral : 5.154 35.223 608 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.00 % Allowed : 19.53 % 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: 1.61 (0.37), residues: 549 helix: 1.63 (0.27), residues: 392 sheet: None (None), residues: 0 loop : -0.27 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 121 TYR 0.017 0.001 TYR A 84 PHE 0.011 0.001 PHE A 110 TRP 0.008 0.001 TRP A 553 HIS 0.002 0.000 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 4580) covalent geometry : angle 0.48522 / 0.25 ( 6248) SS BOND : bond 0.00079 / 0.05 ( 1) SS BOND : angle 1.63477 / 0.64 ( 2) hydrogen bonds : bond 0.04122 / 2.72 ( 292) hydrogen bonds : angle 4.47224 / 3.14 ( 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 61 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.147 Fit side-chains REVERT: A 271 TYR cc_start: 0.8347 (m-80) cc_final: 0.8018 (m-80) REVERT: A 376 ILE cc_start: 0.7296 (mp) cc_final: 0.7003 (mp) REVERT: A 420 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.8252 (m) REVERT: A 434 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8611 (m-30) REVERT: A 459 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: A 590 TYR cc_start: 0.8304 (m-80) cc_final: 0.7544 (m-80) REVERT: A 606 ILE cc_start: 0.8241 (mm) cc_final: 0.7989 (mp) outliers start: 14 outliers final: 7 residues processed: 56 average time/residue: 0.2196 time to fit residues: 13.4955 Evaluate side-chains 56 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 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 336 ASP 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 459 PHE Chi-restraints excluded: chain A residue 508 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 37 optimal weight: 0.0030 chunk 54 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8992 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.124785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.097647 restraints weight = 5211.004| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.74 r_work: 0.2875 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4581 Z= 0.142 Angle : 0.511 6.744 6250 Z= 0.263 Chirality : 0.040 0.149 696 Planarity : 0.004 0.029 759 Dihedral : 5.196 34.300 608 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.79 % Allowed : 19.74 % 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: 1.49 (0.37), residues: 549 helix: 1.56 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -0.35 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 341 TYR 0.020 0.001 TYR A 84 PHE 0.012 0.001 PHE A 94 TRP 0.007 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 4580) covalent geometry : angle 0.50984 / 0.26 ( 6248) SS BOND : bond 0.00082 / 0.05 ( 1) SS BOND : angle 1.89358 / 0.74 ( 2) hydrogen bonds : bond 0.04531 / 2.98 ( 292) hydrogen bonds : angle 4.56455 / 3.22 ( 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: 13 poor density : 46 time to evaluate : 0.154 Fit side-chains REVERT: A 304 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7117 (mm-30) REVERT: A 420 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8183 (m) REVERT: A 434 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8660 (m-30) REVERT: A 459 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: A 590 TYR cc_start: 0.8188 (m-80) cc_final: 0.7344 (m-80) outliers start: 13 outliers final: 8 residues processed: 54 average time/residue: 0.1986 time to fit residues: 11.6847 Evaluate side-chains 57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.096 ------------------------------------------------------------------------------- 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 336 ASP 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 508 MET 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: 3.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.126184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099229 restraints weight = 5168.253| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.74 r_work: 0.2916 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4581 Z= 0.124 Angle : 0.493 6.423 6250 Z= 0.254 Chirality : 0.040 0.145 696 Planarity : 0.004 0.028 759 Dihedral : 5.170 34.868 608 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.58 % Allowed : 20.82 % Favored : 76.61 % 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: 1.56 (0.37), residues: 549 helix: 1.60 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -0.31 (0.49), residues: 158 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 0.011 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/Z covalent geometry : bond 0.00294 / 0.12 ( 4580) covalent geometry : angle 0.49257 / 0.25 ( 6248) SS BOND : bond 0.00087 / 0.05 ( 1) SS BOND : angle 1.74242 / 0.69 ( 2) hydrogen bonds : bond 0.04223 / 2.79 ( 292) hydrogen bonds : angle 4.50596 / 3.17 ( 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 60 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.111 Fit side-chains REVERT: A 271 TYR cc_start: 0.8376 (m-80) cc_final: 0.7963 (m-80) REVERT: A 304 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7017 (mm-30) REVERT: A 420 SER cc_start: 0.8671 (OUTLIER) cc_final: 0.8183 (m) REVERT: A 434 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8637 (m-30) REVERT: A 459 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: A 590 TYR cc_start: 0.8170 (m-80) cc_final: 0.7357 (m-80) outliers start: 12 outliers final: 8 residues processed: 56 average time/residue: 0.2314 time to fit residues: 14.1210 Evaluate side-chains 60 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 336 ASP 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 508 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 6 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.131834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105360 restraints weight = 5142.106| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.74 r_work: 0.2897 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4581 Z= 0.124 Angle : 0.500 6.423 6250 Z= 0.256 Chirality : 0.040 0.144 696 Planarity : 0.004 0.028 759 Dihedral : 5.204 34.897 608 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.36 % Allowed : 21.24 % Favored : 76.39 % 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: 1.60 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -0.27 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 121 TYR 0.018 0.001 TYR A 84 PHE 0.013 0.001 PHE A 408 TRP 0.010 0.001 TRP A 264 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 4580) covalent geometry : angle 0.49909 / 0.26 ( 6248) SS BOND : bond 0.00076 / 0.05 ( 1) SS BOND : angle 1.72759 / 0.68 ( 2) hydrogen bonds : bond 0.04236 / 2.79 ( 292) hydrogen bonds : angle 4.50946 / 3.18 ( 849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1226.66 seconds wall clock time: 21 minutes 39.84 seconds (1299.84 seconds total)