Starting phenix.real_space_refine on Tue Aug 4 15:30:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9b_65769/08_2026/9w9b_65769.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9b_65769/08_2026/9w9b_65769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w9b_65769/08_2026/9w9b_65769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9b_65769/08_2026/9w9b_65769.map" model { file = "/net/cci-nas-00/data/ceres_data/9w9b_65769/08_2026/9w9b_65769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9b_65769/08_2026/9w9b_65769.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.062 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 34 5.16 5 Cl 1 4.86 5 C 2898 2.51 5 N 660 2.21 5 O 722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4315 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4314 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 26, 'TRANS': 509} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.21, per 1000 atoms: 0.28 Number of scatterers: 4315 At special positions: 0 Unit cell: (84.293, 69.355, 87.494, 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 1 17.00 S 34 16.00 O 722 8.00 N 660 7.00 C 2898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 166 " 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: 0.43 Conformation dependent library (CDL) restraints added in 193.5 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 994 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 78.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 40 through 54 Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 60 through 69 removed outlier: 4.048A pdb=" N TYR A 64 " --> pdb=" O TRP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 86 through 101 Processing helix chain 'A' and resid 103 through 112 Processing helix chain 'A' and resid 116 through 134 removed outlier: 4.096A pdb=" N LEU A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE A 134 " --> pdb=" O ASN A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 147 Processing helix chain 'A' and resid 186 through 195 Processing helix chain 'A' and resid 210 through 229 Processing helix chain 'A' and resid 238 through 260 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.711A pdb=" N GLY A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.579A pdb=" N LYS A 279 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.044A pdb=" N TRP A 284 " --> pdb=" O ASP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 309 removed outlier: 4.400A pdb=" N THR A 303 " --> pdb=" O GLN A 299 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 349 removed outlier: 3.725A pdb=" N ASP A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 376 through 411 Processing helix chain 'A' and resid 420 through 437 Processing helix chain 'A' and resid 438 through 441 removed outlier: 3.699A pdb=" N THR A 441 " --> pdb=" O PHE A 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 441' Processing helix chain 'A' and resid 443 through 454 removed outlier: 3.896A pdb=" N ILE A 447 " --> pdb=" O GLY A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 475 removed outlier: 3.640A pdb=" N LEU A 462 " --> pdb=" O GLY A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 490 Processing helix chain 'A' and resid 494 through 503 removed outlier: 4.508A pdb=" N LYS A 498 " --> pdb=" O TRP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 519 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 532 through 548 removed outlier: 4.010A pdb=" N SER A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 564 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 524 through 525 289 hydrogen bonds defined for protein. 852 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: 0.74 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: 1.23 - 1.34: 1251 1.34 - 1.46: 1128 1.46 - 1.58: 2027 1.58 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 4453 Sorted by residual: bond pdb=" C THR A 505 " pdb=" N PRO A 506 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 4.13e-01 bond pdb=" C PHE A 62 " pdb=" N PRO A 63 " ideal model delta sigma weight residual 1.335 1.344 -0.008 1.36e-02 5.41e+03 3.84e-01 bond pdb=" CB CYS A 402 " pdb=" SG CYS A 402 " ideal model delta sigma weight residual 1.808 1.788 0.020 3.30e-02 9.18e+02 3.55e-01 bond pdb=" C LEU A 393 " pdb=" O LEU A 393 " ideal model delta sigma weight residual 1.237 1.230 0.006 1.19e-02 7.06e+03 2.93e-01 bond pdb=" CG PRO A 575 " pdb=" CD PRO A 575 " ideal model delta sigma weight residual 1.503 1.485 0.018 3.40e-02 8.65e+02 2.86e-01 ... (remaining 4448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 5975 1.46 - 2.93: 70 2.93 - 4.39: 12 4.39 - 5.85: 7 5.85 - 7.32: 1 Bond angle restraints: 6065 Sorted by residual: angle pdb=" N PHE A 467 " pdb=" CA PHE A 467 " pdb=" C PHE A 467 " ideal model delta sigma weight residual 111.36 113.65 -2.29 1.09e+00 8.42e-01 4.40e+00 angle pdb=" CA LEU A 271 " pdb=" CB LEU A 271 " pdb=" CG LEU A 271 " ideal model delta sigma weight residual 116.30 123.62 -7.32 3.50e+00 8.16e-02 4.37e+00 angle pdb=" C PRO A 63 " pdb=" N TYR A 64 " pdb=" CA TYR A 64 " ideal model delta sigma weight residual 121.14 117.74 3.40 1.75e+00 3.27e-01 3.76e+00 angle pdb=" N LEU A 271 " pdb=" CA LEU A 271 " pdb=" C LEU A 271 " ideal model delta sigma weight residual 110.80 114.91 -4.11 2.13e+00 2.20e-01 3.73e+00 angle pdb=" N SER A 465 " pdb=" CA SER A 465 " pdb=" C SER A 465 " ideal model delta sigma weight residual 111.36 109.42 1.94 1.09e+00 8.42e-01 3.18e+00 ... (remaining 6060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.10: 2316 13.10 - 26.19: 165 26.19 - 39.29: 42 39.29 - 52.39: 9 52.39 - 65.48: 2 Dihedral angle restraints: 2534 sinusoidal: 977 harmonic: 1557 Sorted by residual: dihedral pdb=" N TYR A 482 " pdb=" CA TYR A 482 " pdb=" CB TYR A 482 " pdb=" CG TYR A 482 " ideal model delta sinusoidal sigma weight residual -60.00 -104.90 44.90 3 1.50e+01 4.44e-03 8.08e+00 dihedral pdb=" CA MET A 387 " pdb=" CB MET A 387 " pdb=" CG MET A 387 " pdb=" SD MET A 387 " ideal model delta sinusoidal sigma weight residual -60.00 -101.91 41.91 3 1.50e+01 4.44e-03 7.51e+00 dihedral pdb=" CA LEU A 120 " pdb=" CB LEU A 120 " pdb=" CG LEU A 120 " pdb=" CD1 LEU A 120 " ideal model delta sinusoidal sigma weight residual 60.00 101.32 -41.32 3 1.50e+01 4.44e-03 7.39e+00 ... (remaining 2531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 358 0.024 - 0.049: 183 0.049 - 0.073: 94 0.073 - 0.097: 27 0.097 - 0.121: 12 Chirality restraints: 674 Sorted by residual: chirality pdb=" CA PRO A 63 " pdb=" N PRO A 63 " pdb=" C PRO A 63 " pdb=" CB PRO A 63 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA PHE A 367 " pdb=" N PHE A 367 " pdb=" C PHE A 367 " pdb=" CB PHE A 367 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.61e-01 chirality pdb=" CA VAL A 350 " pdb=" N VAL A 350 " pdb=" C VAL A 350 " pdb=" CB VAL A 350 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 ... (remaining 671 not shown) Planarity restraints: 738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 350 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO A 351 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 351 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 351 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 191 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.65e+00 pdb=" C PHE A 191 " 0.022 2.00e-02 2.50e+03 pdb=" O PHE A 191 " -0.008 2.00e-02 2.50e+03 pdb=" N TRP A 192 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 471 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C CYS A 471 " 0.018 2.00e-02 2.50e+03 pdb=" O CYS A 471 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE A 472 " -0.006 2.00e-02 2.50e+03 ... (remaining 735 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 2982 3.06 - 3.52: 4807 3.52 - 3.98: 7123 3.98 - 4.44: 8980 4.44 - 4.90: 13442 Nonbonded interactions: 37334 Sorted by model distance: nonbonded pdb=" O ILE A 267 " pdb=" O TYR A 270 " model vdw 2.601 3.040 nonbonded pdb=" N THR A 40 " pdb=" N ASN A 41 " model vdw 2.636 2.560 nonbonded pdb=" N SER A 457 " pdb=" O SER A 457 " model vdw 2.644 2.496 nonbonded pdb=" N ALA A 356 " pdb=" O ALA A 356 " model vdw 2.656 2.496 nonbonded pdb=" N VAL A 350 " pdb=" O VAL A 350 " model vdw 2.661 2.496 ... (remaining 37329 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: 1.660 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.660 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:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.002 0.026 4454 Z= 0.111 Angle : 0.464 7.315 6067 Z= 0.242 Chirality : 0.038 0.121 674 Planarity : 0.003 0.047 738 Dihedral : 10.069 65.481 1537 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % 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: 1.41 (0.36), residues: 532 helix: 1.43 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -0.28 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 256 TYR 0.016 0.001 TYR A 270 PHE 0.011 0.001 PHE A 463 TRP 0.007 0.001 TRP A 534 HIS 0.001 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 4453) covalent geometry : angle 0.46324 / 0.24 ( 6065) SS BOND : bond 0.00082 / 0.04 ( 1) SS BOND : angle 1.74975 / 0.83 ( 2) hydrogen bonds : bond 0.11194 / 6.77 ( 289) hydrogen bonds : angle 5.27180 / 3.86 ( 852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.175 Fit side-chains REVERT: A 189 MET cc_start: 0.8317 (ttp) cc_final: 0.7970 (tpp) REVERT: A 201 SER cc_start: 0.9178 (t) cc_final: 0.8802 (p) REVERT: A 208 SER cc_start: 0.8677 (m) cc_final: 0.8413 (t) REVERT: A 225 TYR cc_start: 0.8666 (t80) cc_final: 0.7614 (t80) REVERT: A 277 ARG cc_start: 0.8433 (mmm-85) cc_final: 0.7958 (tpp-160) REVERT: A 282 GLN cc_start: 0.8498 (tt0) cc_final: 0.8237 (tt0) REVERT: A 309 ASN cc_start: 0.8243 (m-40) cc_final: 0.7866 (m-40) REVERT: A 394 ASP cc_start: 0.7117 (m-30) cc_final: 0.6721 (m-30) REVERT: A 465 SER cc_start: 0.8993 (t) cc_final: 0.8677 (p) REVERT: A 494 TRP cc_start: 0.7209 (m100) cc_final: 0.6553 (m-10) REVERT: A 566 ARG cc_start: 0.6964 (mtt90) cc_final: 0.6547 (mmm160) REVERT: A 567 LYS cc_start: 0.7967 (tmtm) cc_final: 0.7567 (tptp) REVERT: A 571 GLN cc_start: 0.8254 (tt0) cc_final: 0.8017 (tt0) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.3969 time to fit residues: 37.5677 Evaluate side-chains 67 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.133222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109429 restraints weight = 5531.290| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.13 r_work: 0.3180 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4454 Z= 0.140 Angle : 0.510 7.319 6067 Z= 0.261 Chirality : 0.040 0.127 674 Planarity : 0.004 0.044 738 Dihedral : 3.903 13.608 580 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.70 % Allowed : 10.85 % Favored : 87.45 % 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 (0.36), residues: 532 helix: 1.62 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.52 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 109 TYR 0.020 0.001 TYR A 64 PHE 0.012 0.001 PHE A 463 TRP 0.007 0.001 TRP A 534 HIS 0.001 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 4453) covalent geometry : angle 0.50945 / 0.26 ( 6065) SS BOND : bond 0.00026 / 0.01 ( 1) SS BOND : angle 1.82918 / 0.86 ( 2) hydrogen bonds : bond 0.04179 / 2.71 ( 289) hydrogen bonds : angle 4.55741 / 3.34 ( 852) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: A 126 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7929 (mt-10) REVERT: A 189 MET cc_start: 0.8127 (ttp) cc_final: 0.7746 (tpp) REVERT: A 201 SER cc_start: 0.9154 (t) cc_final: 0.8729 (p) REVERT: A 208 SER cc_start: 0.8556 (m) cc_final: 0.8245 (t) REVERT: A 225 TYR cc_start: 0.8617 (t80) cc_final: 0.7412 (t80) REVERT: A 277 ARG cc_start: 0.8332 (mmm-85) cc_final: 0.7924 (tpp-160) REVERT: A 282 GLN cc_start: 0.8425 (tt0) cc_final: 0.8201 (tt0) REVERT: A 309 ASN cc_start: 0.8230 (m-40) cc_final: 0.7934 (m-40) REVERT: A 389 ILE cc_start: 0.8742 (mt) cc_final: 0.8422 (mp) REVERT: A 394 ASP cc_start: 0.6927 (m-30) cc_final: 0.6507 (m-30) REVERT: A 466 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7901 (tp) REVERT: A 488 MET cc_start: 0.8550 (mtm) cc_final: 0.8255 (mtm) REVERT: A 494 TRP cc_start: 0.7101 (m100) cc_final: 0.6422 (m-10) REVERT: A 566 ARG cc_start: 0.6758 (mtt90) cc_final: 0.6291 (mmm160) REVERT: A 567 LYS cc_start: 0.7896 (tmtm) cc_final: 0.7490 (tptp) REVERT: A 571 GLN cc_start: 0.8320 (tt0) cc_final: 0.8009 (tt0) outliers start: 8 outliers final: 3 residues processed: 80 average time/residue: 0.3092 time to fit residues: 25.9920 Evaluate side-chains 71 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 518 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 47 optimal weight: 0.0970 chunk 46 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.133499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109720 restraints weight = 5469.486| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.13 r_work: 0.3186 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4454 Z= 0.129 Angle : 0.498 7.107 6067 Z= 0.252 Chirality : 0.039 0.132 674 Planarity : 0.004 0.042 738 Dihedral : 3.885 14.036 580 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.91 % Allowed : 11.06 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.36), residues: 532 helix: 1.74 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.53 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 109 TYR 0.017 0.001 TYR A 64 PHE 0.018 0.001 PHE A 45 TRP 0.008 0.001 TRP A 534 HIS 0.001 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 4453) covalent geometry : angle 0.49720 / 0.25 ( 6065) SS BOND : bond 0.00001 / 0.00 ( 1) SS BOND : angle 1.74878 / 0.82 ( 2) hydrogen bonds : bond 0.03952 / 2.58 ( 289) hydrogen bonds : angle 4.42969 / 3.24 ( 852) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 126 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7844 (mt-10) REVERT: A 189 MET cc_start: 0.8199 (ttp) cc_final: 0.7814 (tpp) REVERT: A 201 SER cc_start: 0.9152 (t) cc_final: 0.8723 (p) REVERT: A 208 SER cc_start: 0.8542 (m) cc_final: 0.8243 (t) REVERT: A 277 ARG cc_start: 0.8355 (mmm-85) cc_final: 0.8000 (tpp-160) REVERT: A 309 ASN cc_start: 0.8219 (m-40) cc_final: 0.7904 (m-40) REVERT: A 389 ILE cc_start: 0.8738 (mt) cc_final: 0.8419 (mp) REVERT: A 466 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7893 (tp) REVERT: A 494 TRP cc_start: 0.7085 (m100) cc_final: 0.6400 (m-10) REVERT: A 562 ARG cc_start: 0.8293 (ptp-110) cc_final: 0.7592 (mmp80) REVERT: A 566 ARG cc_start: 0.6722 (mtt90) cc_final: 0.6272 (mmm160) REVERT: A 567 LYS cc_start: 0.7865 (tmtm) cc_final: 0.7455 (tptp) REVERT: A 571 GLN cc_start: 0.8306 (tt0) cc_final: 0.7994 (tt0) outliers start: 9 outliers final: 5 residues processed: 79 average time/residue: 0.4479 time to fit residues: 37.0080 Evaluate side-chains 72 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 548 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 36 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.108916 restraints weight = 5468.709| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.11 r_work: 0.3166 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4454 Z= 0.137 Angle : 0.507 9.552 6067 Z= 0.255 Chirality : 0.040 0.132 674 Planarity : 0.004 0.043 738 Dihedral : 3.911 14.313 580 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.91 % Allowed : 12.34 % Favored : 85.74 % 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: 1.72 (0.36), residues: 532 helix: 1.73 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.49 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 109 TYR 0.017 0.001 TYR A 64 PHE 0.011 0.001 PHE A 463 TRP 0.007 0.001 TRP A 534 HIS 0.001 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 4453) covalent geometry : angle 0.50625 / 0.25 ( 6065) SS BOND : bond 0.00000 / 0.00 ( 1) SS BOND : angle 1.85063 / 0.87 ( 2) hydrogen bonds : bond 0.03976 / 2.59 ( 289) hydrogen bonds : angle 4.41782 / 3.23 ( 852) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.173 Fit side-chains REVERT: A 126 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7921 (mt-10) REVERT: A 151 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: A 189 MET cc_start: 0.8221 (ttp) cc_final: 0.7837 (tpp) REVERT: A 201 SER cc_start: 0.9165 (t) cc_final: 0.8732 (p) REVERT: A 208 SER cc_start: 0.8542 (m) cc_final: 0.8242 (t) REVERT: A 277 ARG cc_start: 0.8358 (mmm-85) cc_final: 0.8058 (tpp-160) REVERT: A 282 GLN cc_start: 0.8326 (tt0) cc_final: 0.7459 (tm-30) REVERT: A 309 ASN cc_start: 0.8241 (m-40) cc_final: 0.7954 (m-40) REVERT: A 389 ILE cc_start: 0.8757 (mt) cc_final: 0.8435 (mp) REVERT: A 466 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7934 (tp) REVERT: A 494 TRP cc_start: 0.7117 (m100) cc_final: 0.6413 (m-10) REVERT: A 562 ARG cc_start: 0.8310 (ptp-110) cc_final: 0.7588 (mmp80) REVERT: A 566 ARG cc_start: 0.6744 (mtt90) cc_final: 0.6243 (mmm160) REVERT: A 567 LYS cc_start: 0.7845 (tmtm) cc_final: 0.7449 (tptp) REVERT: A 571 GLN cc_start: 0.8320 (tt0) cc_final: 0.8000 (tt0) outliers start: 9 outliers final: 4 residues processed: 80 average time/residue: 0.4168 time to fit residues: 34.9313 Evaluate side-chains 68 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 548 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 14 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.132692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.108818 restraints weight = 5516.995| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.13 r_work: 0.3160 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4454 Z= 0.137 Angle : 0.507 9.304 6067 Z= 0.256 Chirality : 0.040 0.141 674 Planarity : 0.004 0.044 738 Dihedral : 3.921 14.487 580 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.34 % Allowed : 13.19 % Favored : 84.47 % 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: 1.79 (0.36), residues: 532 helix: 1.79 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.46 (0.49), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 109 TYR 0.017 0.001 TYR A 64 PHE 0.018 0.001 PHE A 45 TRP 0.007 0.001 TRP A 534 HIS 0.001 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 4453) covalent geometry : angle 0.50620 / 0.26 ( 6065) SS BOND : bond 0.00002 / 0.00 ( 1) SS BOND : angle 1.81813 / 0.86 ( 2) hydrogen bonds : bond 0.03924 / 2.57 ( 289) hydrogen bonds : angle 4.40715 / 3.23 ( 852) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5865 (mp0) REVERT: A 52 GLU cc_start: 0.6619 (mt-10) cc_final: 0.6264 (tm-30) REVERT: A 151 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: A 189 MET cc_start: 0.8164 (ttp) cc_final: 0.7822 (tpp) REVERT: A 201 SER cc_start: 0.9162 (t) cc_final: 0.8682 (p) REVERT: A 208 SER cc_start: 0.8541 (m) cc_final: 0.8245 (t) REVERT: A 277 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.8073 (tpp-160) REVERT: A 282 GLN cc_start: 0.8344 (tt0) cc_final: 0.7490 (tm-30) REVERT: A 285 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7417 (tmm) REVERT: A 309 ASN cc_start: 0.8253 (m-40) cc_final: 0.7963 (m-40) REVERT: A 389 ILE cc_start: 0.8754 (mt) cc_final: 0.8434 (mp) REVERT: A 466 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7906 (tp) REVERT: A 494 TRP cc_start: 0.7129 (m100) cc_final: 0.6424 (m-10) REVERT: A 562 ARG cc_start: 0.8304 (ptp-110) cc_final: 0.7598 (mmp80) REVERT: A 566 ARG cc_start: 0.6768 (mtt90) cc_final: 0.6264 (mmm160) REVERT: A 567 LYS cc_start: 0.7875 (tmtm) cc_final: 0.7447 (tptp) REVERT: A 571 GLN cc_start: 0.8322 (tt0) cc_final: 0.7916 (tt0) outliers start: 11 outliers final: 5 residues processed: 75 average time/residue: 0.4770 time to fit residues: 37.3646 Evaluate side-chains 71 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 548 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 23 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.133035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109022 restraints weight = 5573.534| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.13 r_work: 0.3166 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4454 Z= 0.129 Angle : 0.504 8.810 6067 Z= 0.253 Chirality : 0.039 0.125 674 Planarity : 0.004 0.044 738 Dihedral : 3.903 14.220 580 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.91 % Allowed : 14.47 % Favored : 83.62 % 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: 1.84 (0.36), residues: 532 helix: 1.84 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.48 (0.49), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 109 TYR 0.017 0.001 TYR A 64 PHE 0.011 0.001 PHE A 463 TRP 0.007 0.001 TRP A 534 HIS 0.001 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 4453) covalent geometry : angle 0.50326 / 0.25 ( 6065) SS BOND : bond 0.00024 / 0.01 ( 1) SS BOND : angle 1.74237 / 0.82 ( 2) hydrogen bonds : bond 0.03878 / 2.53 ( 289) hydrogen bonds : angle 4.36760 / 3.20 ( 852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.097 Fit side-chains REVERT: A 44 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5875 (mp0) REVERT: A 52 GLU cc_start: 0.6597 (mt-10) cc_final: 0.6276 (tm-30) REVERT: A 151 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: A 189 MET cc_start: 0.8249 (ttp) cc_final: 0.7881 (tpp) REVERT: A 201 SER cc_start: 0.9164 (t) cc_final: 0.8685 (p) REVERT: A 208 SER cc_start: 0.8557 (m) cc_final: 0.8265 (t) REVERT: A 225 TYR cc_start: 0.8781 (t80) cc_final: 0.7436 (t80) REVERT: A 277 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.8105 (tpp-160) REVERT: A 282 GLN cc_start: 0.8360 (tt0) cc_final: 0.7506 (tm-30) REVERT: A 285 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7513 (tmm) REVERT: A 309 ASN cc_start: 0.8247 (m-40) cc_final: 0.7935 (m-40) REVERT: A 389 ILE cc_start: 0.8779 (mt) cc_final: 0.8455 (mp) REVERT: A 394 ASP cc_start: 0.6959 (m-30) cc_final: 0.6560 (m-30) REVERT: A 420 ARG cc_start: 0.6663 (mmt180) cc_final: 0.6208 (mmt180) REVERT: A 466 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7952 (tp) REVERT: A 494 TRP cc_start: 0.7122 (m100) cc_final: 0.6426 (m-10) REVERT: A 562 ARG cc_start: 0.8341 (ptp-110) cc_final: 0.7651 (mmp80) REVERT: A 566 ARG cc_start: 0.6768 (mtt90) cc_final: 0.6301 (mmm160) REVERT: A 567 LYS cc_start: 0.7876 (tmtm) cc_final: 0.7474 (tptp) REVERT: A 571 GLN cc_start: 0.8306 (tt0) cc_final: 0.7981 (tt0) outliers start: 9 outliers final: 5 residues processed: 75 average time/residue: 0.4593 time to fit residues: 36.0061 Evaluate side-chains 73 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 548 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 14 optimal weight: 0.1980 chunk 43 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.0030 chunk 16 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 overall best weight: 0.3190 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.135155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111288 restraints weight = 5509.501| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.12 r_work: 0.3200 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4454 Z= 0.106 Angle : 0.489 8.568 6067 Z= 0.243 Chirality : 0.039 0.139 674 Planarity : 0.004 0.043 738 Dihedral : 3.815 13.411 580 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.13 % Allowed : 14.68 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.36), residues: 532 helix: 1.92 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.47 (0.49), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 109 TYR 0.014 0.001 TYR A 64 PHE 0.020 0.001 PHE A 45 TRP 0.008 0.001 TRP A 534 HIS 0.001 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 4453) covalent geometry : angle 0.48865 / 0.24 ( 6065) SS BOND : bond 0.00010 / 0.01 ( 1) SS BOND : angle 1.38074 / 0.66 ( 2) hydrogen bonds : bond 0.03647 / 2.39 ( 289) hydrogen bonds : angle 4.27805 / 3.13 ( 852) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 44 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5783 (mp0) REVERT: A 151 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7533 (pm20) REVERT: A 189 MET cc_start: 0.8238 (ttp) cc_final: 0.7858 (tpp) REVERT: A 201 SER cc_start: 0.9148 (t) cc_final: 0.8674 (p) REVERT: A 208 SER cc_start: 0.8550 (m) cc_final: 0.8276 (t) REVERT: A 247 TYR cc_start: 0.8060 (m-80) cc_final: 0.7322 (m-80) REVERT: A 277 ARG cc_start: 0.8377 (mmm-85) cc_final: 0.8158 (tpp-160) REVERT: A 282 GLN cc_start: 0.8331 (tt0) cc_final: 0.7509 (tm-30) REVERT: A 285 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7513 (tmm) REVERT: A 309 ASN cc_start: 0.8195 (m-40) cc_final: 0.7810 (m-40) REVERT: A 389 ILE cc_start: 0.8793 (mt) cc_final: 0.8487 (mp) REVERT: A 466 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7965 (tp) REVERT: A 494 TRP cc_start: 0.7117 (m100) cc_final: 0.6347 (m-10) REVERT: A 562 ARG cc_start: 0.8347 (ptp-110) cc_final: 0.7659 (mmp80) REVERT: A 566 ARG cc_start: 0.6732 (mtt90) cc_final: 0.6359 (mmm160) REVERT: A 567 LYS cc_start: 0.7901 (tmtm) cc_final: 0.7478 (tptp) REVERT: A 571 GLN cc_start: 0.8301 (tt0) cc_final: 0.7893 (tt0) outliers start: 10 outliers final: 5 residues processed: 76 average time/residue: 0.4896 time to fit residues: 38.9260 Evaluate side-chains 77 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 548 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109514 restraints weight = 5538.053| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.13 r_work: 0.3164 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4454 Z= 0.135 Angle : 0.513 8.641 6067 Z= 0.256 Chirality : 0.040 0.138 674 Planarity : 0.004 0.044 738 Dihedral : 3.880 13.751 580 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.77 % Allowed : 14.47 % Favored : 82.77 % 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: 1.86 (0.36), residues: 532 helix: 1.84 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.47 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 109 TYR 0.017 0.001 TYR A 64 PHE 0.011 0.001 PHE A 463 TRP 0.009 0.001 TRP A 154 HIS 0.001 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 4453) covalent geometry : angle 0.51188 / 0.26 ( 6065) SS BOND : bond 0.00021 / 0.01 ( 1) SS BOND : angle 1.54847 / 0.74 ( 2) hydrogen bonds : bond 0.03866 / 2.53 ( 289) hydrogen bonds : angle 4.37077 / 3.19 ( 852) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.162 Fit side-chains REVERT: A 44 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5836 (mp0) REVERT: A 151 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7555 (pm20) REVERT: A 189 MET cc_start: 0.8255 (ttp) cc_final: 0.7966 (tpp) REVERT: A 201 SER cc_start: 0.9162 (t) cc_final: 0.8676 (p) REVERT: A 208 SER cc_start: 0.8502 (m) cc_final: 0.8210 (t) REVERT: A 247 TYR cc_start: 0.8090 (m-80) cc_final: 0.7308 (m-80) REVERT: A 277 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.8152 (tpp-160) REVERT: A 282 GLN cc_start: 0.8328 (tt0) cc_final: 0.7480 (tm-30) REVERT: A 285 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7419 (tmm) REVERT: A 309 ASN cc_start: 0.8252 (m-40) cc_final: 0.7937 (m-40) REVERT: A 389 ILE cc_start: 0.8775 (mt) cc_final: 0.8458 (mp) REVERT: A 420 ARG cc_start: 0.6700 (mmt180) cc_final: 0.6387 (mmt180) REVERT: A 465 SER cc_start: 0.8875 (t) cc_final: 0.8493 (p) REVERT: A 466 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7911 (tp) REVERT: A 494 TRP cc_start: 0.7078 (m100) cc_final: 0.6338 (m-10) REVERT: A 562 ARG cc_start: 0.8336 (ptp-110) cc_final: 0.7646 (mmp80) REVERT: A 566 ARG cc_start: 0.6784 (mtt90) cc_final: 0.6407 (mmm160) REVERT: A 567 LYS cc_start: 0.7885 (tmtm) cc_final: 0.7525 (mmmt) REVERT: A 571 GLN cc_start: 0.8317 (tt0) cc_final: 0.7965 (tt0) outliers start: 13 outliers final: 7 residues processed: 79 average time/residue: 0.4104 time to fit residues: 34.0665 Evaluate side-chains 77 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 548 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 36 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 12 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.6562 > 50:) chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.132775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108708 restraints weight = 5578.840| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.15 r_work: 0.3149 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4454 Z= 0.142 Angle : 0.535 8.623 6067 Z= 0.263 Chirality : 0.040 0.127 674 Planarity : 0.004 0.045 738 Dihedral : 3.928 14.124 580 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.77 % Allowed : 14.89 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.36), residues: 532 helix: 1.79 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.49 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 109 TYR 0.018 0.001 TYR A 64 PHE 0.022 0.001 PHE A 45 TRP 0.008 0.001 TRP A 154 HIS 0.001 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 4453) covalent geometry : angle 0.53405 / 0.26 ( 6065) SS BOND : bond 0.00027 / 0.01 ( 1) SS BOND : angle 1.68657 / 0.80 ( 2) hydrogen bonds : bond 0.03943 / 2.57 ( 289) hydrogen bonds : angle 4.41413 / 3.23 ( 852) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.156 Fit side-chains REVERT: A 44 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.5804 (mp0) REVERT: A 52 GLU cc_start: 0.6472 (mt-10) cc_final: 0.6183 (tm-30) REVERT: A 151 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7462 (pm20) REVERT: A 189 MET cc_start: 0.8278 (ttp) cc_final: 0.7914 (tpp) REVERT: A 201 SER cc_start: 0.9160 (t) cc_final: 0.8670 (p) REVERT: A 208 SER cc_start: 0.8504 (m) cc_final: 0.8199 (t) REVERT: A 277 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.8139 (tpp-160) REVERT: A 282 GLN cc_start: 0.8331 (tt0) cc_final: 0.7476 (tm-30) REVERT: A 285 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7491 (tmm) REVERT: A 389 ILE cc_start: 0.8763 (mt) cc_final: 0.8443 (mp) REVERT: A 420 ARG cc_start: 0.6717 (mmt180) cc_final: 0.6444 (mmt180) REVERT: A 466 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7932 (tp) REVERT: A 494 TRP cc_start: 0.7120 (m100) cc_final: 0.6355 (m-10) REVERT: A 562 ARG cc_start: 0.8336 (ptp-110) cc_final: 0.7638 (mmp80) REVERT: A 566 ARG cc_start: 0.6750 (mtt90) cc_final: 0.6358 (mmm160) REVERT: A 567 LYS cc_start: 0.7910 (tmtm) cc_final: 0.7520 (mmmt) REVERT: A 571 GLN cc_start: 0.8318 (tt0) cc_final: 0.7904 (tt0) outliers start: 13 outliers final: 7 residues processed: 78 average time/residue: 0.4487 time to fit residues: 36.6291 Evaluate side-chains 78 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 548 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 0.0470 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 0.0270 chunk 42 optimal weight: 0.5980 overall best weight: 0.3336 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.135219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111510 restraints weight = 5486.250| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.12 r_work: 0.3198 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4454 Z= 0.110 Angle : 0.519 8.382 6067 Z= 0.255 Chirality : 0.039 0.133 674 Planarity : 0.004 0.043 738 Dihedral : 3.864 16.250 580 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.34 % Allowed : 15.74 % Favored : 81.91 % 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: 1.89 (0.36), residues: 532 helix: 1.87 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.47 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 109 TYR 0.014 0.001 TYR A 64 PHE 0.010 0.001 PHE A 463 TRP 0.008 0.001 TRP A 534 HIS 0.001 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 4453) covalent geometry : angle 0.51888 / 0.26 ( 6065) SS BOND : bond 0.00017 / 0.01 ( 1) SS BOND : angle 1.25189 / 0.61 ( 2) hydrogen bonds : bond 0.03694 / 2.42 ( 289) hydrogen bonds : angle 4.32705 / 3.16 ( 852) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.162 Fit side-chains REVERT: A 44 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.6034 (mp0) REVERT: A 151 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7430 (pm20) REVERT: A 189 MET cc_start: 0.8327 (ttp) cc_final: 0.7895 (tpp) REVERT: A 201 SER cc_start: 0.9122 (t) cc_final: 0.8633 (p) REVERT: A 208 SER cc_start: 0.8478 (m) cc_final: 0.8183 (t) REVERT: A 247 TYR cc_start: 0.8042 (m-80) cc_final: 0.7272 (m-80) REVERT: A 277 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.8153 (tpp-160) REVERT: A 282 GLN cc_start: 0.8305 (tt0) cc_final: 0.7451 (tm-30) REVERT: A 285 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7497 (tmm) REVERT: A 389 ILE cc_start: 0.8735 (mt) cc_final: 0.8423 (mp) REVERT: A 420 ARG cc_start: 0.6653 (mmt180) cc_final: 0.6365 (mmt180) REVERT: A 465 SER cc_start: 0.8843 (t) cc_final: 0.8455 (p) REVERT: A 466 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7868 (tp) REVERT: A 494 TRP cc_start: 0.7054 (m100) cc_final: 0.6317 (m-10) REVERT: A 562 ARG cc_start: 0.8282 (ptp-110) cc_final: 0.7647 (mmp80) REVERT: A 566 ARG cc_start: 0.6660 (mtt90) cc_final: 0.6383 (mmm160) REVERT: A 567 LYS cc_start: 0.7886 (tmtm) cc_final: 0.7550 (mmmt) REVERT: A 571 GLN cc_start: 0.8284 (tt0) cc_final: 0.7953 (tt0) REVERT: A 577 SER cc_start: 0.8911 (t) cc_final: 0.8635 (p) outliers start: 11 outliers final: 6 residues processed: 75 average time/residue: 0.4361 time to fit residues: 34.3812 Evaluate side-chains 79 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 548 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.133229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.109377 restraints weight = 5534.821| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.13 r_work: 0.3171 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4454 Z= 0.135 Angle : 0.551 8.517 6067 Z= 0.269 Chirality : 0.041 0.137 674 Planarity : 0.004 0.045 738 Dihedral : 3.934 17.423 580 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.13 % Allowed : 15.74 % Favored : 82.13 % 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: 1.77 (0.36), residues: 532 helix: 1.77 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -0.48 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 109 TYR 0.017 0.001 TYR A 64 PHE 0.022 0.001 PHE A 45 TRP 0.008 0.001 TRP A 154 HIS 0.001 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 4453) covalent geometry : angle 0.55058 / 0.27 ( 6065) SS BOND : bond 0.00058 / 0.03 ( 1) SS BOND : angle 1.60655 / 0.75 ( 2) hydrogen bonds : bond 0.03916 / 2.54 ( 289) hydrogen bonds : angle 4.40912 / 3.22 ( 852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1619.40 seconds wall clock time: 28 minutes 24.41 seconds (1704.41 seconds total)