Starting phenix.real_space_refine on Sat Apr 4 22:10:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmm_66097/04_2026/9wmm_66097_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmm_66097/04_2026/9wmm_66097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wmm_66097/04_2026/9wmm_66097_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmm_66097/04_2026/9wmm_66097_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wmm_66097/04_2026/9wmm_66097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmm_66097/04_2026/9wmm_66097.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.119 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 3062 2.51 5 N 657 2.21 5 O 734 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-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4489 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4263 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 26, 'TRANS': 513} Chain breaks: 1 Chain: "A" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 226 Unusual residues: {' CL': 1, ' NA': 1, 'CLR': 3, 'Y01': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 1.14, per 1000 atoms: 0.25 Number of scatterers: 4489 At special positions: 0 Unit cell: (82.159, 73.623, 73.623, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 1 11.00 O 734 8.00 N 657 7.00 C 3062 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: 0.49 Conformation dependent library (CDL) restraints added in 381.9 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 982 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 78.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.538A pdb=" N LEU A 44 " --> pdb=" O TRP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 72 through 86 Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 86 through 102 removed outlier: 3.547A pdb=" N LEU A 90 " --> pdb=" O CYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.601A pdb=" N TRP A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 115 through 147 removed outlier: 3.994A pdb=" N GLY A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 4.190A pdb=" N HIS A 156 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 214 through 234 Processing helix chain 'A' and resid 247 through 264 removed outlier: 3.517A pdb=" N THR A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 removed outlier: 4.042A pdb=" N GLY A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 284 through 300 removed outlier: 4.242A pdb=" N TRP A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.824A pdb=" N TYR A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 353 Processing helix chain 'A' and resid 365 through 376 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 380 through 415 removed outlier: 3.563A pdb=" N TRP A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 439 Processing helix chain 'A' and resid 440 through 443 removed outlier: 3.792A pdb=" N THR A 443 " --> pdb=" O ILE A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.643A pdb=" N TRP A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 532 through 561 removed outlier: 3.839A pdb=" N SER A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Proline residue: A 551 - end of helix Processing helix chain 'A' and resid 564 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 525 through 526 290 hydrogen bonds defined for protein. 846 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: 0.69 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 638 1.31 - 1.44: 1322 1.44 - 1.56: 2625 1.56 - 1.69: 2 1.69 - 1.81: 54 Bond restraints: 4641 Sorted by residual: bond pdb=" C SER A 381 " pdb=" O SER A 381 " ideal model delta sigma weight residual 1.238 1.186 0.052 1.28e-02 6.10e+03 1.66e+01 bond pdb=" N SER A 381 " pdb=" CA SER A 381 " ideal model delta sigma weight residual 1.457 1.505 -0.049 1.41e-02 5.03e+03 1.19e+01 bond pdb=" N ILE A 325 " pdb=" CA ILE A 325 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.19e-02 7.06e+03 1.13e+01 bond pdb=" N VAL A 592 " pdb=" CA VAL A 592 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.25e-02 6.40e+03 9.64e+00 bond pdb=" N GLN A 522 " pdb=" CA GLN A 522 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.05e-02 9.07e+03 9.63e+00 ... (remaining 4636 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 5946 1.69 - 3.37: 335 3.37 - 5.06: 69 5.06 - 6.75: 10 6.75 - 8.43: 5 Bond angle restraints: 6365 Sorted by residual: angle pdb=" N ARG A 321 " pdb=" CA ARG A 321 " pdb=" C ARG A 321 " ideal model delta sigma weight residual 111.11 105.41 5.70 1.20e+00 6.94e-01 2.26e+01 angle pdb=" CA LEU A 395 " pdb=" C LEU A 395 " pdb=" O LEU A 395 " ideal model delta sigma weight residual 120.82 116.30 4.52 1.05e+00 9.07e-01 1.85e+01 angle pdb=" CA SER A 298 " pdb=" C SER A 298 " pdb=" O SER A 298 " ideal model delta sigma weight residual 120.82 116.63 4.19 1.05e+00 9.07e-01 1.59e+01 angle pdb=" CA LEU A 503 " pdb=" C LEU A 503 " pdb=" O LEU A 503 " ideal model delta sigma weight residual 120.42 116.29 4.13 1.06e+00 8.90e-01 1.51e+01 angle pdb=" N ALA A 74 " pdb=" CA ALA A 74 " pdb=" C ALA A 74 " ideal model delta sigma weight residual 111.71 107.36 4.35 1.15e+00 7.56e-01 1.43e+01 ... (remaining 6360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.49: 2702 24.49 - 48.98: 222 48.98 - 73.47: 32 73.47 - 97.96: 13 97.96 - 122.45: 6 Dihedral angle restraints: 2975 sinusoidal: 1425 harmonic: 1550 Sorted by residual: dihedral pdb=" C10 CLR A 703 " pdb=" C1 CLR A 703 " pdb=" C2 CLR A 703 " pdb=" C3 CLR A 703 " ideal model delta sinusoidal sigma weight residual -56.83 65.62 -122.45 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C10 CLR A 709 " pdb=" C1 CLR A 709 " pdb=" C2 CLR A 709 " pdb=" C3 CLR A 709 " ideal model delta sinusoidal sigma weight residual -56.83 65.36 -122.19 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C10 CLR A 706 " pdb=" C1 CLR A 706 " pdb=" C2 CLR A 706 " pdb=" C3 CLR A 706 " ideal model delta sinusoidal sigma weight residual -56.83 63.18 -120.01 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 2972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 614 0.062 - 0.125: 96 0.125 - 0.187: 16 0.187 - 0.249: 2 0.249 - 0.311: 2 Chirality restraints: 730 Sorted by residual: chirality pdb=" CBE Y01 A 704 " pdb=" CAP Y01 A 704 " pdb=" CBB Y01 A 704 " pdb=" CBI Y01 A 704 " both_signs ideal model delta sigma weight residual False 2.57 2.26 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C8 CLR A 703 " pdb=" C14 CLR A 703 " pdb=" C7 CLR A 703 " pdb=" C9 CLR A 703 " both_signs ideal model delta sigma weight residual False 2.69 2.39 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA ASN A 134 " pdb=" N ASN A 134 " pdb=" C ASN A 134 " pdb=" CB ASN A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 727 not shown) Planarity restraints: 734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 321 " 0.019 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ARG A 321 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG A 321 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP A 322 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 522 " 0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO A 523 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 523 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 523 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 471 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C LEU A 471 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU A 471 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 472 " -0.015 2.00e-02 2.50e+03 ... (remaining 731 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1560 2.86 - 3.37: 4544 3.37 - 3.88: 8039 3.88 - 4.39: 9746 4.39 - 4.90: 15810 Nonbonded interactions: 39699 Sorted by model distance: nonbonded pdb=" O LEU A 144 " pdb=" OG SER A 147 " model vdw 2.345 3.040 nonbonded pdb=" OG SER A 298 " pdb="NA NA A 701 " model vdw 2.354 2.470 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 536 " model vdw 2.383 3.040 nonbonded pdb=" OD1 ASN A 59 " pdb="NA NA A 701 " model vdw 2.424 2.470 nonbonded pdb=" O PHE A 339 " pdb=" OG SER A 343 " model vdw 2.433 3.040 ... (remaining 39694 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: 1.540 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.230 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:7.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 4642 Z= 0.337 Angle : 0.892 8.434 6367 Z= 0.536 Chirality : 0.050 0.311 730 Planarity : 0.006 0.065 734 Dihedral : 18.537 122.446 1990 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 19.65 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.35), residues: 536 helix: 0.93 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.41 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.016 0.002 TYR A 132 PHE 0.012 0.001 PHE A 245 TRP 0.027 0.002 TRP A 215 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 4641) covalent geometry : angle 0.89172 ( 6365) SS BOND : bond 0.00289 ( 1) SS BOND : angle 0.51790 ( 2) hydrogen bonds : bond 0.12558 ( 290) hydrogen bonds : angle 5.90014 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.159 Fit side-chains REVERT: A 155 GLU cc_start: 0.8696 (tt0) cc_final: 0.8436 (tt0) REVERT: A 358 GLN cc_start: 0.8044 (pt0) cc_final: 0.7754 (pt0) REVERT: A 398 ASP cc_start: 0.7105 (m-30) cc_final: 0.6868 (m-30) REVERT: A 434 MET cc_start: 0.8645 (mtt) cc_final: 0.8394 (mtt) REVERT: A 489 MET cc_start: 0.8935 (ttp) cc_final: 0.8527 (mtm) REVERT: A 554 MET cc_start: 0.8627 (mtt) cc_final: 0.8405 (mtt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.4948 time to fit residues: 55.6046 Evaluate side-chains 76 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.0470 chunk 19 optimal weight: 0.9980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.144987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131401 restraints weight = 5153.304| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.47 r_work: 0.3483 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4642 Z= 0.135 Angle : 0.648 9.236 6367 Z= 0.296 Chirality : 0.041 0.242 730 Planarity : 0.005 0.047 734 Dihedral : 11.014 64.936 1063 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.19 % Allowed : 18.32 % Favored : 77.48 % 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: 1.52 (0.36), residues: 536 helix: 1.83 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -1.02 (0.47), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 420 TYR 0.014 0.001 TYR A 132 PHE 0.015 0.001 PHE A 245 TRP 0.014 0.001 TRP A 215 HIS 0.001 0.000 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4641) covalent geometry : angle 0.64766 ( 6365) SS BOND : bond 0.00170 ( 1) SS BOND : angle 0.18023 ( 2) hydrogen bonds : bond 0.04645 ( 290) hydrogen bonds : angle 4.64521 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.145 Fit side-chains REVERT: A 40 TRP cc_start: 0.6572 (t60) cc_final: 0.6208 (t-100) REVERT: A 43 LYS cc_start: 0.8038 (mptt) cc_final: 0.7674 (mptt) REVERT: A 133 TYR cc_start: 0.7451 (m-10) cc_final: 0.7091 (m-80) REVERT: A 309 PHE cc_start: 0.4935 (t80) cc_final: 0.3940 (t80) REVERT: A 317 GLN cc_start: 0.8508 (tt0) cc_final: 0.8270 (tt0) REVERT: A 339 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7195 (t80) REVERT: A 358 GLN cc_start: 0.8314 (pt0) cc_final: 0.8110 (pt0) REVERT: A 489 MET cc_start: 0.9006 (ttp) cc_final: 0.8491 (mtm) REVERT: A 525 GLU cc_start: 0.8101 (pt0) cc_final: 0.7593 (pm20) REVERT: A 554 MET cc_start: 0.8555 (mtt) cc_final: 0.8324 (mtt) outliers start: 19 outliers final: 5 residues processed: 93 average time/residue: 0.5044 time to fit residues: 48.7387 Evaluate side-chains 81 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 578 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126685 restraints weight = 5229.018| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.49 r_work: 0.3426 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4642 Z= 0.156 Angle : 0.605 6.532 6367 Z= 0.280 Chirality : 0.040 0.267 730 Planarity : 0.004 0.035 734 Dihedral : 10.048 58.946 1063 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.21 % Allowed : 19.21 % Favored : 78.59 % 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 (0.36), residues: 536 helix: 1.88 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -0.85 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 530 TYR 0.017 0.002 TYR A 132 PHE 0.011 0.001 PHE A 460 TRP 0.011 0.001 TRP A 225 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 4641) covalent geometry : angle 0.60476 ( 6365) SS BOND : bond 0.00131 ( 1) SS BOND : angle 0.20520 ( 2) hydrogen bonds : bond 0.04664 ( 290) hydrogen bonds : angle 4.54593 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.140 Fit side-chains REVERT: A 40 TRP cc_start: 0.6568 (t60) cc_final: 0.6194 (t-100) REVERT: A 43 LYS cc_start: 0.8260 (mptt) cc_final: 0.7801 (mptt) REVERT: A 53 TYR cc_start: 0.7281 (t80) cc_final: 0.6789 (t80) REVERT: A 133 TYR cc_start: 0.7365 (m-10) cc_final: 0.6763 (m-80) REVERT: A 278 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7794 (mt0) REVERT: A 309 PHE cc_start: 0.5025 (t80) cc_final: 0.4064 (t80) REVERT: A 317 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8446 (tt0) REVERT: A 358 GLN cc_start: 0.8405 (pt0) cc_final: 0.8171 (pt0) REVERT: A 456 TYR cc_start: 0.8746 (m-80) cc_final: 0.7567 (m-80) REVERT: A 489 MET cc_start: 0.9022 (ttp) cc_final: 0.8604 (mtm) REVERT: A 525 GLU cc_start: 0.8107 (pt0) cc_final: 0.7639 (pm20) REVERT: A 554 MET cc_start: 0.8635 (mtt) cc_final: 0.8399 (mtt) outliers start: 10 outliers final: 2 residues processed: 87 average time/residue: 0.4449 time to fit residues: 40.4811 Evaluate side-chains 76 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124939 restraints weight = 5185.582| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.38 r_work: 0.3377 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4642 Z= 0.148 Angle : 0.570 6.030 6367 Z= 0.267 Chirality : 0.039 0.258 730 Planarity : 0.004 0.036 734 Dihedral : 10.045 57.759 1063 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.31 % Allowed : 18.32 % Favored : 78.37 % 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: 1.78 (0.36), residues: 536 helix: 1.96 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -0.76 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 321 TYR 0.016 0.001 TYR A 132 PHE 0.012 0.001 PHE A 91 TRP 0.010 0.001 TRP A 225 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 4641) covalent geometry : angle 0.56963 ( 6365) SS BOND : bond 0.00135 ( 1) SS BOND : angle 0.18702 ( 2) hydrogen bonds : bond 0.04499 ( 290) hydrogen bonds : angle 4.47500 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.167 Fit side-chains REVERT: A 40 TRP cc_start: 0.6565 (t60) cc_final: 0.6218 (t-100) REVERT: A 43 LYS cc_start: 0.8349 (mptt) cc_final: 0.7898 (mptt) REVERT: A 53 TYR cc_start: 0.7601 (t80) cc_final: 0.7261 (t80) REVERT: A 133 TYR cc_start: 0.7529 (m-10) cc_final: 0.6950 (m-80) REVERT: A 278 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7933 (mt0) REVERT: A 309 PHE cc_start: 0.4933 (t80) cc_final: 0.4013 (t80) REVERT: A 317 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8446 (tt0) REVERT: A 358 GLN cc_start: 0.8468 (pt0) cc_final: 0.8256 (pt0) REVERT: A 456 TYR cc_start: 0.8731 (m-80) cc_final: 0.7666 (m-80) REVERT: A 489 MET cc_start: 0.8986 (ttp) cc_final: 0.8586 (mtm) REVERT: A 525 GLU cc_start: 0.8073 (pt0) cc_final: 0.7711 (pm20) REVERT: A 554 MET cc_start: 0.8655 (mtt) cc_final: 0.8447 (mtt) REVERT: A 584 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7523 (tt0) outliers start: 15 outliers final: 4 residues processed: 87 average time/residue: 0.4881 time to fit residues: 44.2991 Evaluate side-chains 80 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 584 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122373 restraints weight = 5212.070| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.43 r_work: 0.3341 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4642 Z= 0.177 Angle : 0.596 6.476 6367 Z= 0.279 Chirality : 0.040 0.281 730 Planarity : 0.004 0.035 734 Dihedral : 10.087 59.453 1063 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.43 % Allowed : 20.09 % Favored : 77.48 % 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: 1.74 (0.36), residues: 536 helix: 1.89 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.66 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 321 TYR 0.017 0.002 TYR A 132 PHE 0.011 0.001 PHE A 389 TRP 0.011 0.001 TRP A 225 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 4641) covalent geometry : angle 0.59588 ( 6365) SS BOND : bond 0.00112 ( 1) SS BOND : angle 0.35503 ( 2) hydrogen bonds : bond 0.04730 ( 290) hydrogen bonds : angle 4.56002 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.164 Fit side-chains REVERT: A 40 TRP cc_start: 0.6531 (t60) cc_final: 0.6140 (t-100) REVERT: A 43 LYS cc_start: 0.8468 (mptt) cc_final: 0.8029 (mptt) REVERT: A 133 TYR cc_start: 0.7662 (m-10) cc_final: 0.7104 (m-80) REVERT: A 278 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7967 (mt0) REVERT: A 280 HIS cc_start: 0.8148 (p-80) cc_final: 0.7885 (p90) REVERT: A 317 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8481 (tt0) REVERT: A 456 TYR cc_start: 0.8734 (m-80) cc_final: 0.7731 (m-80) REVERT: A 489 MET cc_start: 0.9033 (ttp) cc_final: 0.8623 (mtm) REVERT: A 525 GLU cc_start: 0.8102 (pt0) cc_final: 0.7720 (pm20) outliers start: 11 outliers final: 3 residues processed: 81 average time/residue: 0.4494 time to fit residues: 38.1210 Evaluate side-chains 74 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 546 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125069 restraints weight = 5203.718| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.40 r_work: 0.3383 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4642 Z= 0.129 Angle : 0.544 5.364 6367 Z= 0.256 Chirality : 0.038 0.250 730 Planarity : 0.004 0.037 734 Dihedral : 9.970 59.250 1063 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.65 % Allowed : 18.98 % Favored : 78.37 % 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: 1.94 (0.36), residues: 536 helix: 2.05 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -0.59 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 321 TYR 0.015 0.001 TYR A 132 PHE 0.008 0.001 PHE A 91 TRP 0.009 0.001 TRP A 225 HIS 0.002 0.000 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4641) covalent geometry : angle 0.54401 ( 6365) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.17732 ( 2) hydrogen bonds : bond 0.04340 ( 290) hydrogen bonds : angle 4.40869 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.167 Fit side-chains REVERT: A 40 TRP cc_start: 0.6494 (t60) cc_final: 0.6108 (t-100) REVERT: A 43 LYS cc_start: 0.8419 (mptt) cc_final: 0.7973 (mptt) REVERT: A 53 TYR cc_start: 0.6958 (t80) cc_final: 0.6737 (t80) REVERT: A 133 TYR cc_start: 0.7654 (m-10) cc_final: 0.6966 (m-80) REVERT: A 278 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7924 (mt0) REVERT: A 280 HIS cc_start: 0.8088 (p-80) cc_final: 0.7826 (p90) REVERT: A 309 PHE cc_start: 0.5066 (t80) cc_final: 0.4161 (t80) REVERT: A 317 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: A 456 TYR cc_start: 0.8643 (m-80) cc_final: 0.7738 (m-80) REVERT: A 489 MET cc_start: 0.9034 (ttp) cc_final: 0.8648 (mtm) REVERT: A 525 GLU cc_start: 0.8046 (pt0) cc_final: 0.7703 (pm20) outliers start: 12 outliers final: 7 residues processed: 90 average time/residue: 0.4399 time to fit residues: 41.4490 Evaluate side-chains 79 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.125325 restraints weight = 5226.488| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.43 r_work: 0.3382 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4642 Z= 0.130 Angle : 0.541 5.222 6367 Z= 0.256 Chirality : 0.038 0.201 730 Planarity : 0.004 0.036 734 Dihedral : 10.016 59.235 1063 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.21 % Allowed : 19.87 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.36), residues: 536 helix: 2.08 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -0.46 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 321 TYR 0.016 0.001 TYR A 132 PHE 0.007 0.001 PHE A 389 TRP 0.010 0.001 TRP A 225 HIS 0.002 0.000 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4641) covalent geometry : angle 0.54147 ( 6365) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.19602 ( 2) hydrogen bonds : bond 0.04341 ( 290) hydrogen bonds : angle 4.38764 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.109 Fit side-chains REVERT: A 40 TRP cc_start: 0.6536 (t60) cc_final: 0.6168 (t-100) REVERT: A 43 LYS cc_start: 0.8472 (mptt) cc_final: 0.8029 (mptt) REVERT: A 91 PHE cc_start: 0.7865 (t80) cc_final: 0.7530 (t80) REVERT: A 133 TYR cc_start: 0.7744 (m-10) cc_final: 0.7150 (m-80) REVERT: A 278 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: A 280 HIS cc_start: 0.8135 (p-80) cc_final: 0.7882 (p90) REVERT: A 309 PHE cc_start: 0.5135 (t80) cc_final: 0.4266 (t80) REVERT: A 317 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: A 456 TYR cc_start: 0.8630 (m-80) cc_final: 0.7795 (m-80) REVERT: A 489 MET cc_start: 0.9019 (ttp) cc_final: 0.8660 (mtm) REVERT: A 525 GLU cc_start: 0.8037 (pt0) cc_final: 0.7753 (pm20) outliers start: 10 outliers final: 5 residues processed: 85 average time/residue: 0.4676 time to fit residues: 41.4860 Evaluate side-chains 80 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 546 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 31 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124179 restraints weight = 5217.201| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.40 r_work: 0.3370 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4642 Z= 0.146 Angle : 0.558 5.831 6367 Z= 0.264 Chirality : 0.039 0.219 730 Planarity : 0.004 0.035 734 Dihedral : 9.867 59.787 1063 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.99 % Allowed : 18.98 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.36), residues: 536 helix: 2.05 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.44 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 321 TYR 0.016 0.001 TYR A 132 PHE 0.008 0.001 PHE A 389 TRP 0.010 0.001 TRP A 225 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4641) covalent geometry : angle 0.55797 ( 6365) SS BOND : bond 0.00084 ( 1) SS BOND : angle 0.25468 ( 2) hydrogen bonds : bond 0.04423 ( 290) hydrogen bonds : angle 4.41407 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.160 Fit side-chains REVERT: A 40 TRP cc_start: 0.6531 (t60) cc_final: 0.6154 (t-100) REVERT: A 43 LYS cc_start: 0.8444 (mptt) cc_final: 0.7998 (mptt) REVERT: A 133 TYR cc_start: 0.7699 (m-10) cc_final: 0.7114 (m-80) REVERT: A 278 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7951 (mt0) REVERT: A 280 HIS cc_start: 0.8139 (p-80) cc_final: 0.7886 (p90) REVERT: A 309 PHE cc_start: 0.5111 (t80) cc_final: 0.4236 (t80) REVERT: A 317 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: A 456 TYR cc_start: 0.8610 (m-80) cc_final: 0.7750 (m-80) REVERT: A 489 MET cc_start: 0.9046 (ttp) cc_final: 0.8681 (mtm) REVERT: A 525 GLU cc_start: 0.8126 (pt0) cc_final: 0.7744 (pm20) outliers start: 9 outliers final: 5 residues processed: 79 average time/residue: 0.4712 time to fit residues: 38.8414 Evaluate side-chains 76 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 546 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 0.0670 chunk 45 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124991 restraints weight = 5183.619| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.42 r_work: 0.3376 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4642 Z= 0.133 Angle : 0.542 5.215 6367 Z= 0.258 Chirality : 0.038 0.200 730 Planarity : 0.004 0.036 734 Dihedral : 9.824 59.707 1063 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.55 % Allowed : 19.43 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.36), residues: 536 helix: 2.03 (0.25), residues: 380 sheet: None (None), residues: 0 loop : -0.37 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 530 TYR 0.016 0.001 TYR A 132 PHE 0.011 0.001 PHE A 91 TRP 0.010 0.001 TRP A 225 HIS 0.002 0.000 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4641) covalent geometry : angle 0.54172 ( 6365) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.23682 ( 2) hydrogen bonds : bond 0.04332 ( 290) hydrogen bonds : angle 4.39393 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.162 Fit side-chains REVERT: A 40 TRP cc_start: 0.6547 (t60) cc_final: 0.6176 (t-100) REVERT: A 43 LYS cc_start: 0.8496 (mptt) cc_final: 0.8080 (mptt) REVERT: A 133 TYR cc_start: 0.7750 (m-10) cc_final: 0.7158 (m-80) REVERT: A 278 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7987 (mt0) REVERT: A 280 HIS cc_start: 0.8145 (p-80) cc_final: 0.7901 (p90) REVERT: A 309 PHE cc_start: 0.5124 (t80) cc_final: 0.4220 (t80) REVERT: A 317 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: A 398 ASP cc_start: 0.6959 (m-30) cc_final: 0.6747 (m-30) REVERT: A 456 TYR cc_start: 0.8585 (m-80) cc_final: 0.7721 (m-80) REVERT: A 489 MET cc_start: 0.9015 (ttp) cc_final: 0.8674 (mtm) REVERT: A 525 GLU cc_start: 0.8125 (pt0) cc_final: 0.7755 (pm20) outliers start: 7 outliers final: 5 residues processed: 78 average time/residue: 0.4639 time to fit residues: 37.8400 Evaluate side-chains 75 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 546 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 0.0070 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 3 optimal weight: 0.0670 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128554 restraints weight = 5145.928| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.39 r_work: 0.3422 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4642 Z= 0.109 Angle : 0.512 5.173 6367 Z= 0.245 Chirality : 0.037 0.166 730 Planarity : 0.004 0.037 734 Dihedral : 9.651 59.352 1063 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.32 % Allowed : 19.65 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.36), residues: 536 helix: 2.15 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -0.33 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 321 TYR 0.014 0.001 TYR A 320 PHE 0.007 0.001 PHE A 245 TRP 0.011 0.001 TRP A 534 HIS 0.002 0.000 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 4641) covalent geometry : angle 0.51245 ( 6365) SS BOND : bond 0.00035 ( 1) SS BOND : angle 0.22522 ( 2) hydrogen bonds : bond 0.03978 ( 290) hydrogen bonds : angle 4.28081 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 40 TRP cc_start: 0.6533 (t60) cc_final: 0.6168 (t-100) REVERT: A 43 LYS cc_start: 0.8408 (mptt) cc_final: 0.7993 (mptt) REVERT: A 53 TYR cc_start: 0.6726 (t80) cc_final: 0.6526 (t80) REVERT: A 133 TYR cc_start: 0.7558 (m-10) cc_final: 0.6989 (m-80) REVERT: A 278 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7890 (mt0) REVERT: A 309 PHE cc_start: 0.4952 (t80) cc_final: 0.4120 (t80) REVERT: A 317 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: A 456 TYR cc_start: 0.8507 (m-80) cc_final: 0.7659 (m-80) REVERT: A 489 MET cc_start: 0.8942 (ttp) cc_final: 0.8622 (ttp) REVERT: A 525 GLU cc_start: 0.8179 (pt0) cc_final: 0.7736 (pm20) outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 0.4604 time to fit residues: 39.4746 Evaluate side-chains 79 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 546 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 0.0060 chunk 7 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126496 restraints weight = 5142.598| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.42 r_work: 0.3395 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4642 Z= 0.131 Angle : 0.535 5.856 6367 Z= 0.254 Chirality : 0.038 0.187 730 Planarity : 0.004 0.036 734 Dihedral : 9.601 59.239 1063 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.10 % Allowed : 20.31 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.36), residues: 536 helix: 2.14 (0.25), residues: 380 sheet: None (None), residues: 0 loop : -0.35 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 530 TYR 0.016 0.001 TYR A 132 PHE 0.010 0.001 PHE A 91 TRP 0.009 0.001 TRP A 225 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4641) covalent geometry : angle 0.53458 ( 6365) SS BOND : bond 0.00061 ( 1) SS BOND : angle 0.24984 ( 2) hydrogen bonds : bond 0.04161 ( 290) hydrogen bonds : angle 4.32213 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1678.20 seconds wall clock time: 29 minutes 14.87 seconds (1754.87 seconds total)