Starting phenix.real_space_refine on Wed Mar 4 01:34:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wnx_32634/03_2026/7wnx_32634.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wnx_32634/03_2026/7wnx_32634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wnx_32634/03_2026/7wnx_32634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wnx_32634/03_2026/7wnx_32634.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wnx_32634/03_2026/7wnx_32634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wnx_32634/03_2026/7wnx_32634.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5250 atoms to isotropic. 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 28 5.16 5 Cl 1 4.86 5 C 3654 2.51 5 N 933 2.21 5 O 1025 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5643 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5606 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 37, 'TRANS': 696} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'1I2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.37, per 1000 atoms: 0.24 Number of scatterers: 5643 At special positions: 0 Unit cell: (77.08, 77.9, 115.62, 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 28 16.00 F 2 9.00 O 1025 8.00 N 933 7.00 C 3654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 151.7 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 5 sheets defined 69.2% alpha, 2.6% 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 -2 through 12 Processing helix chain 'A' and resid 14 through 32 Processing helix chain 'A' and resid 48 through 61 removed outlier: 3.864A pdb=" N ALA A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 101 removed outlier: 3.757A pdb=" N HIS A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 143 through 160 Proline residue: A 156 - end of helix removed outlier: 3.862A pdb=" N GLN A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 206 Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 208 through 234 Proline residue: A 214 - end of helix removed outlier: 4.195A pdb=" N GLU A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 250 removed outlier: 4.202A pdb=" N VAL A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 269 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 274 through 302 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 309 through 342 removed outlier: 3.755A pdb=" N LYS A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 346 removed outlier: 3.973A pdb=" N ASP A 346 " --> pdb=" O PRO A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 346' Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 401 through 415 Proline residue: A 407 - end of helix Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 436 through 449 removed outlier: 3.571A pdb=" N GLN A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 482 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.938A pdb=" N LYS A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 581 Proline residue: A 565 - end of helix Processing helix chain 'A' and resid 586 through 612 removed outlier: 3.945A pdb=" N ILE A 590 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.673A pdb=" N MET A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 659 removed outlier: 4.185A pdb=" N GLY A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 695 removed outlier: 4.844A pdb=" N ARG A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 731 removed outlier: 3.630A pdb=" N ILE A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Proline residue: A 725 - end of helix Processing helix chain 'A' and resid 739 through 748 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA3, first strand: chain 'A' and resid 424 through 425 Processing sheet with id=AA4, first strand: chain 'A' and resid 461 through 462 Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 500 376 hydrogen bonds defined for protein. 1086 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: 0.81 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 933 1.31 - 1.43: 1411 1.43 - 1.56: 3361 1.56 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 5760 Sorted by residual: bond pdb=" C02 1I2 A1101 " pdb=" N24 1I2 A1101 " ideal model delta sigma weight residual 1.340 1.449 -0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C14 1I2 A1101 " pdb=" C15 1I2 A1101 " ideal model delta sigma weight residual 1.465 1.531 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C18 1I2 A1101 " pdb="CL1 1I2 A1101 " ideal model delta sigma weight residual 1.731 1.783 -0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" C29 1I2 A1101 " pdb=" C30 1I2 A1101 " ideal model delta sigma weight residual 1.530 1.479 0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" C14 1I2 A1101 " pdb=" N05 1I2 A1101 " ideal model delta sigma weight residual 1.364 1.313 0.051 2.00e-02 2.50e+03 6.53e+00 ... (remaining 5755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 7570 1.57 - 3.14: 206 3.14 - 4.71: 48 4.71 - 6.28: 16 6.28 - 7.85: 2 Bond angle restraints: 7842 Sorted by residual: angle pdb=" C GLY A 732 " pdb=" N ASP A 733 " pdb=" CA ASP A 733 " ideal model delta sigma weight residual 121.54 128.22 -6.68 1.91e+00 2.74e-01 1.22e+01 angle pdb=" CA CYS A 735 " pdb=" C CYS A 735 " pdb=" O CYS A 735 " ideal model delta sigma weight residual 121.34 117.69 3.65 1.18e+00 7.18e-01 9.59e+00 angle pdb=" C26 1I2 A1101 " pdb=" N27 1I2 A1101 " pdb=" C28 1I2 A1101 " ideal model delta sigma weight residual 117.38 109.53 7.85 3.00e+00 1.11e-01 6.85e+00 angle pdb=" CA ASP A 256 " pdb=" C ASP A 256 " pdb=" O ASP A 256 " ideal model delta sigma weight residual 120.82 118.15 2.67 1.05e+00 9.07e-01 6.49e+00 angle pdb=" C ASP A 77 " pdb=" N ASP A 78 " pdb=" CA ASP A 78 " ideal model delta sigma weight residual 121.54 126.32 -4.78 1.91e+00 2.74e-01 6.26e+00 ... (remaining 7837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 3062 17.00 - 34.00: 316 34.00 - 51.00: 65 51.00 - 68.00: 11 68.00 - 85.00: 7 Dihedral angle restraints: 3461 sinusoidal: 1372 harmonic: 2089 Sorted by residual: dihedral pdb=" CA THR A 82 " pdb=" C THR A 82 " pdb=" N ASP A 83 " pdb=" CA ASP A 83 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ARG A 720 " pdb=" C ARG A 720 " pdb=" N MET A 721 " pdb=" CA MET A 721 " ideal model delta harmonic sigma weight residual -180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ASP A 83 " pdb=" CB ASP A 83 " pdb=" CG ASP A 83 " pdb=" OD1 ASP A 83 " ideal model delta sinusoidal sigma weight residual -30.00 -88.43 58.43 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 3458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 651 0.040 - 0.080: 215 0.080 - 0.120: 60 0.120 - 0.160: 4 0.160 - 0.200: 2 Chirality restraints: 932 Sorted by residual: chirality pdb=" CA TRP A 736 " pdb=" N TRP A 736 " pdb=" C TRP A 736 " pdb=" CB TRP A 736 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" C28 1I2 A1101 " pdb=" C29 1I2 A1101 " pdb=" C31 1I2 A1101 " pdb=" N27 1I2 A1101 " both_signs ideal model delta sigma weight residual False -2.57 -2.40 -0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CB VAL A 587 " pdb=" CA VAL A 587 " pdb=" CG1 VAL A 587 " pdb=" CG2 VAL A 587 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 929 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 720 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C ARG A 720 " 0.041 2.00e-02 2.50e+03 pdb=" O ARG A 720 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 721 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 736 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C TRP A 736 " 0.040 2.00e-02 2.50e+03 pdb=" O TRP A 736 " -0.016 2.00e-02 2.50e+03 pdb=" N TRP A 737 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 716 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C ALA A 716 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA A 716 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 717 " -0.013 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 695 2.75 - 3.29: 5970 3.29 - 3.82: 9120 3.82 - 4.36: 9884 4.36 - 4.90: 17766 Nonbonded interactions: 43435 Sorted by model distance: nonbonded pdb=" O GLN A 140 " pdb=" ND2 ASN A 150 " model vdw 2.209 3.120 nonbonded pdb=" OE1 GLN A 49 " pdb=" NH1 ARG A 534 " model vdw 2.215 3.120 nonbonded pdb=" O GLN A 87 " pdb=" OG1 THR A 91 " model vdw 2.262 3.040 nonbonded pdb=" NH2 ARG A 65 " pdb=" O GLY A 141 " model vdw 2.272 3.120 nonbonded pdb=" NH1 ARG A 230 " pdb=" OE2 GLU A 234 " model vdw 2.282 3.120 ... (remaining 43430 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.820 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.004 0.109 5760 Z= 0.217 Angle : 0.677 7.850 7842 Z= 0.370 Chirality : 0.042 0.200 932 Planarity : 0.005 0.040 990 Dihedral : 14.539 85.001 2117 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.22 % Favored : 91.51 % Rotamer: Outliers : 0.50 % Allowed : 7.01 % Favored : 92.49 % 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: -2.32 (0.29), residues: 730 helix: -0.72 (0.22), residues: 465 sheet: -3.34 (0.63), residues: 41 loop : -2.71 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 288 TYR 0.013 0.001 TYR A 10 PHE 0.015 0.001 PHE A 12 TRP 0.008 0.001 TRP A 736 HIS 0.001 0.000 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 5760) covalent geometry : angle 0.67650 ( 7842) hydrogen bonds : bond 0.12278 ( 376) hydrogen bonds : angle 5.69542 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 0.190 Fit side-chains REVERT: A 13 ARG cc_start: 0.7708 (pmt170) cc_final: 0.7408 (ptp90) REVERT: A 284 MET cc_start: 0.6768 (mtp) cc_final: 0.6483 (mtp) REVERT: A 444 GLN cc_start: 0.8687 (tp40) cc_final: 0.8472 (tt0) REVERT: A 620 MET cc_start: 0.8321 (mmm) cc_final: 0.8086 (mmm) REVERT: A 662 MET cc_start: 0.7842 (mpp) cc_final: 0.7520 (mpp) REVERT: A 669 ARG cc_start: 0.8787 (ttp80) cc_final: 0.8279 (ttm110) REVERT: A 736 TRP cc_start: 0.8328 (OUTLIER) cc_final: 0.7345 (m100) outliers start: 3 outliers final: 1 residues processed: 122 average time/residue: 0.0727 time to fit residues: 11.6544 Evaluate side-chains 90 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 87 GLN A 132 HIS ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.130269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.096373 restraints weight = 9002.768| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.88 r_work: 0.3117 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5760 Z= 0.133 Angle : 0.605 7.198 7842 Z= 0.310 Chirality : 0.040 0.129 932 Planarity : 0.005 0.053 990 Dihedral : 5.538 54.052 827 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.00 % Allowed : 14.02 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.32), residues: 730 helix: 0.90 (0.25), residues: 469 sheet: -3.04 (0.68), residues: 43 loop : -2.46 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.013 0.001 TYR A 10 PHE 0.012 0.001 PHE A 12 TRP 0.006 0.001 TRP A 108 HIS 0.002 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 5760) covalent geometry : angle 0.60512 ( 7842) hydrogen bonds : bond 0.04547 ( 376) hydrogen bonds : angle 4.91512 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.191 Fit side-chains REVERT: A 284 MET cc_start: 0.6974 (mtp) cc_final: 0.6671 (mtp) REVERT: A 444 GLN cc_start: 0.8805 (tp40) cc_final: 0.8478 (tt0) REVERT: A 499 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8429 (mtpp) REVERT: A 620 MET cc_start: 0.8696 (mmm) cc_final: 0.8458 (mmm) REVERT: A 662 MET cc_start: 0.8026 (mpp) cc_final: 0.7682 (mpp) REVERT: A 669 ARG cc_start: 0.8856 (ttp80) cc_final: 0.8314 (ttm110) REVERT: A 736 TRP cc_start: 0.8111 (OUTLIER) cc_final: 0.6255 (m100) outliers start: 12 outliers final: 5 residues processed: 112 average time/residue: 0.0713 time to fit residues: 10.5925 Evaluate side-chains 93 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 14 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 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 = 0.3671 r_free = 0.3671 target = 0.126945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.092241 restraints weight = 9010.516| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.89 r_work: 0.3049 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5760 Z= 0.183 Angle : 0.640 8.365 7842 Z= 0.322 Chirality : 0.042 0.140 932 Planarity : 0.005 0.054 990 Dihedral : 5.606 58.614 827 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.67 % Allowed : 19.70 % Favored : 77.63 % 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: -0.06 (0.33), residues: 730 helix: 1.17 (0.25), residues: 481 sheet: -2.90 (0.68), residues: 43 loop : -2.32 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 463 TYR 0.017 0.001 TYR A 10 PHE 0.025 0.002 PHE A 202 TRP 0.005 0.001 TRP A 498 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 5760) covalent geometry : angle 0.63957 ( 7842) hydrogen bonds : bond 0.05021 ( 376) hydrogen bonds : angle 4.93281 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.200 Fit side-chains REVERT: A 13 ARG cc_start: 0.7767 (pmt170) cc_final: 0.7371 (ptp90) REVERT: A 284 MET cc_start: 0.7072 (mtp) cc_final: 0.6785 (mtp) REVERT: A 390 TRP cc_start: 0.7426 (OUTLIER) cc_final: 0.6765 (m-90) REVERT: A 398 MET cc_start: 0.8579 (tpp) cc_final: 0.8028 (tmm) REVERT: A 444 GLN cc_start: 0.8825 (tp40) cc_final: 0.8513 (tt0) REVERT: A 499 LYS cc_start: 0.8730 (ttmt) cc_final: 0.8431 (mtpp) REVERT: A 523 ARG cc_start: 0.8419 (tpt-90) cc_final: 0.8145 (tpt-90) REVERT: A 620 MET cc_start: 0.8726 (mmm) cc_final: 0.8486 (mmm) REVERT: A 662 MET cc_start: 0.8135 (mpp) cc_final: 0.7640 (mpp) REVERT: A 669 ARG cc_start: 0.8819 (ttp80) cc_final: 0.8256 (ttm110) REVERT: A 736 TRP cc_start: 0.7978 (OUTLIER) cc_final: 0.6414 (m100) outliers start: 16 outliers final: 11 residues processed: 99 average time/residue: 0.0779 time to fit residues: 10.1811 Evaluate side-chains 97 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 0.0060 chunk 31 optimal weight: 1.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 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 = 0.3674 r_free = 0.3674 target = 0.127414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.092389 restraints weight = 9038.893| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.02 r_work: 0.3047 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5760 Z= 0.174 Angle : 0.618 7.026 7842 Z= 0.313 Chirality : 0.041 0.130 932 Planarity : 0.005 0.053 990 Dihedral : 5.371 52.947 827 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.67 % Allowed : 20.03 % Favored : 76.29 % 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: 0.19 (0.33), residues: 730 helix: 1.33 (0.25), residues: 481 sheet: -2.66 (0.67), residues: 46 loop : -2.14 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 660 TYR 0.015 0.001 TYR A 10 PHE 0.015 0.001 PHE A 12 TRP 0.005 0.001 TRP A 108 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 5760) covalent geometry : angle 0.61823 ( 7842) hydrogen bonds : bond 0.04967 ( 376) hydrogen bonds : angle 4.87045 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.203 Fit side-chains REVERT: A 13 ARG cc_start: 0.7762 (pmt170) cc_final: 0.7423 (ptp90) REVERT: A 284 MET cc_start: 0.7066 (mtp) cc_final: 0.6771 (mtp) REVERT: A 390 TRP cc_start: 0.7411 (OUTLIER) cc_final: 0.6689 (m-90) REVERT: A 398 MET cc_start: 0.8592 (tpp) cc_final: 0.8040 (tmm) REVERT: A 444 GLN cc_start: 0.8816 (tp40) cc_final: 0.8508 (tt0) REVERT: A 540 HIS cc_start: 0.8038 (t70) cc_final: 0.7433 (t-90) REVERT: A 620 MET cc_start: 0.8773 (mmm) cc_final: 0.8517 (mmm) REVERT: A 660 ARG cc_start: 0.8304 (mpp80) cc_final: 0.7940 (mpp80) REVERT: A 662 MET cc_start: 0.8114 (mpp) cc_final: 0.7748 (mpp) REVERT: A 669 ARG cc_start: 0.8815 (ttp80) cc_final: 0.8250 (ttm110) REVERT: A 736 TRP cc_start: 0.7922 (OUTLIER) cc_final: 0.6618 (m100) outliers start: 22 outliers final: 12 residues processed: 106 average time/residue: 0.0722 time to fit residues: 10.0982 Evaluate side-chains 97 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 58 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 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 = 0.3685 r_free = 0.3685 target = 0.128493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.093354 restraints weight = 9273.062| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.08 r_work: 0.3063 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5760 Z= 0.148 Angle : 0.605 6.350 7842 Z= 0.305 Chirality : 0.041 0.141 932 Planarity : 0.004 0.054 990 Dihedral : 5.077 53.798 826 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.51 % Allowed : 20.53 % Favored : 75.96 % 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: 0.44 (0.33), residues: 730 helix: 1.53 (0.25), residues: 478 sheet: -2.53 (0.68), residues: 46 loop : -2.02 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 653 TYR 0.018 0.001 TYR A 10 PHE 0.010 0.001 PHE A 134 TRP 0.005 0.001 TRP A 108 HIS 0.001 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 5760) covalent geometry : angle 0.60501 ( 7842) hydrogen bonds : bond 0.04722 ( 376) hydrogen bonds : angle 4.80544 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.214 Fit side-chains REVERT: A 13 ARG cc_start: 0.7700 (pmt170) cc_final: 0.7382 (ptp90) REVERT: A 284 MET cc_start: 0.7031 (mtp) cc_final: 0.6735 (mtp) REVERT: A 346 ASP cc_start: 0.8312 (m-30) cc_final: 0.7356 (t0) REVERT: A 390 TRP cc_start: 0.7399 (OUTLIER) cc_final: 0.6577 (m-90) REVERT: A 398 MET cc_start: 0.8580 (tpp) cc_final: 0.8019 (tmm) REVERT: A 444 GLN cc_start: 0.8802 (tp40) cc_final: 0.8515 (tt0) REVERT: A 540 HIS cc_start: 0.8062 (t70) cc_final: 0.7443 (t-90) REVERT: A 620 MET cc_start: 0.8770 (mmm) cc_final: 0.8498 (mmm) REVERT: A 662 MET cc_start: 0.8107 (mpp) cc_final: 0.7793 (mmt) REVERT: A 669 ARG cc_start: 0.8789 (ttp80) cc_final: 0.8222 (ttm110) REVERT: A 686 LEU cc_start: 0.8942 (mp) cc_final: 0.8643 (mp) REVERT: A 721 MET cc_start: 0.8047 (ptp) cc_final: 0.7631 (ptt) REVERT: A 736 TRP cc_start: 0.7873 (OUTLIER) cc_final: 0.6545 (m100) outliers start: 21 outliers final: 16 residues processed: 106 average time/residue: 0.0732 time to fit residues: 10.4464 Evaluate side-chains 102 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 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 = 0.3669 r_free = 0.3669 target = 0.127030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.092411 restraints weight = 9027.144| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.90 r_work: 0.3049 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5760 Z= 0.176 Angle : 0.620 6.243 7842 Z= 0.313 Chirality : 0.041 0.151 932 Planarity : 0.004 0.037 990 Dihedral : 5.116 53.872 826 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 4.84 % Allowed : 20.87 % Favored : 74.29 % 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: 0.51 (0.33), residues: 730 helix: 1.55 (0.25), residues: 478 sheet: -2.43 (0.70), residues: 46 loop : -1.91 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 660 TYR 0.019 0.001 TYR A 10 PHE 0.011 0.001 PHE A 12 TRP 0.005 0.001 TRP A 736 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 5760) covalent geometry : angle 0.62024 ( 7842) hydrogen bonds : bond 0.04962 ( 376) hydrogen bonds : angle 4.84911 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.205 Fit side-chains REVERT: A 13 ARG cc_start: 0.7776 (pmt170) cc_final: 0.7504 (ptp90) REVERT: A 284 MET cc_start: 0.7070 (mtp) cc_final: 0.6622 (mtp) REVERT: A 325 LEU cc_start: 0.8787 (tt) cc_final: 0.8533 (tt) REVERT: A 346 ASP cc_start: 0.8283 (m-30) cc_final: 0.7357 (t0) REVERT: A 390 TRP cc_start: 0.7480 (OUTLIER) cc_final: 0.6659 (m-90) REVERT: A 398 MET cc_start: 0.8589 (tpp) cc_final: 0.8045 (tmm) REVERT: A 444 GLN cc_start: 0.8828 (tp40) cc_final: 0.8556 (tt0) REVERT: A 540 HIS cc_start: 0.8016 (t70) cc_final: 0.7404 (t-90) REVERT: A 620 MET cc_start: 0.8748 (mmm) cc_final: 0.8464 (mmm) REVERT: A 662 MET cc_start: 0.7947 (mpp) cc_final: 0.7506 (mpp) REVERT: A 669 ARG cc_start: 0.8814 (ttp80) cc_final: 0.8193 (ttp-110) REVERT: A 686 LEU cc_start: 0.8973 (mp) cc_final: 0.8673 (mp) REVERT: A 721 MET cc_start: 0.8035 (ptp) cc_final: 0.7623 (ptm) REVERT: A 736 TRP cc_start: 0.7903 (OUTLIER) cc_final: 0.6517 (m100) outliers start: 29 outliers final: 22 residues processed: 110 average time/residue: 0.0690 time to fit residues: 10.3067 Evaluate side-chains 109 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 706 PHE Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.095826 restraints weight = 9128.527| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.06 r_work: 0.3102 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5760 Z= 0.128 Angle : 0.621 10.276 7842 Z= 0.307 Chirality : 0.041 0.184 932 Planarity : 0.004 0.060 990 Dihedral : 4.935 55.675 826 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.67 % Allowed : 23.87 % Favored : 73.46 % 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: 0.71 (0.34), residues: 730 helix: 1.71 (0.25), residues: 477 sheet: -2.35 (0.71), residues: 46 loop : -1.82 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 478 TYR 0.015 0.001 TYR A 10 PHE 0.035 0.001 PHE A 202 TRP 0.006 0.001 TRP A 108 HIS 0.001 0.000 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5760) covalent geometry : angle 0.62119 ( 7842) hydrogen bonds : bond 0.04231 ( 376) hydrogen bonds : angle 4.77158 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.213 Fit side-chains REVERT: A 13 ARG cc_start: 0.7609 (pmt170) cc_final: 0.7347 (ptp90) REVERT: A 284 MET cc_start: 0.6963 (mtp) cc_final: 0.6670 (mtp) REVERT: A 346 ASP cc_start: 0.8330 (m-30) cc_final: 0.7360 (t0) REVERT: A 390 TRP cc_start: 0.7417 (OUTLIER) cc_final: 0.6605 (m-90) REVERT: A 398 MET cc_start: 0.8538 (tpp) cc_final: 0.8004 (tmm) REVERT: A 444 GLN cc_start: 0.8762 (tp40) cc_final: 0.8481 (tt0) REVERT: A 540 HIS cc_start: 0.8051 (t70) cc_final: 0.7442 (t-90) REVERT: A 620 MET cc_start: 0.8721 (mmm) cc_final: 0.8451 (mmm) REVERT: A 662 MET cc_start: 0.7909 (mpp) cc_final: 0.7580 (mmt) REVERT: A 669 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8184 (ttp-110) REVERT: A 686 LEU cc_start: 0.8931 (mp) cc_final: 0.8616 (mp) REVERT: A 721 MET cc_start: 0.7925 (ptp) cc_final: 0.7511 (ptm) REVERT: A 736 TRP cc_start: 0.7842 (OUTLIER) cc_final: 0.6568 (m100) outliers start: 16 outliers final: 10 residues processed: 109 average time/residue: 0.0669 time to fit residues: 10.0072 Evaluate side-chains 104 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 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 = 0.3709 r_free = 0.3709 target = 0.130649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.095799 restraints weight = 9062.215| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.06 r_work: 0.3104 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5760 Z= 0.128 Angle : 0.627 11.364 7842 Z= 0.307 Chirality : 0.041 0.191 932 Planarity : 0.004 0.039 990 Dihedral : 4.869 55.881 826 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.34 % Allowed : 23.21 % Favored : 73.46 % 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: 0.79 (0.34), residues: 730 helix: 1.74 (0.25), residues: 477 sheet: -2.26 (0.70), residues: 46 loop : -1.73 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 653 TYR 0.015 0.001 TYR A 10 PHE 0.031 0.001 PHE A 202 TRP 0.007 0.001 TRP A 5 HIS 0.001 0.000 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 5760) covalent geometry : angle 0.62708 ( 7842) hydrogen bonds : bond 0.04190 ( 376) hydrogen bonds : angle 4.76494 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.197 Fit side-chains REVERT: A 13 ARG cc_start: 0.7698 (pmt170) cc_final: 0.7461 (ptp90) REVERT: A 284 MET cc_start: 0.6905 (mtp) cc_final: 0.6596 (mtp) REVERT: A 346 ASP cc_start: 0.8286 (m-30) cc_final: 0.7376 (t0) REVERT: A 390 TRP cc_start: 0.7392 (OUTLIER) cc_final: 0.6716 (m-90) REVERT: A 398 MET cc_start: 0.8501 (tpp) cc_final: 0.7984 (tmm) REVERT: A 444 GLN cc_start: 0.8769 (tp40) cc_final: 0.8524 (tt0) REVERT: A 540 HIS cc_start: 0.8038 (t70) cc_final: 0.7424 (t-90) REVERT: A 662 MET cc_start: 0.7935 (mpp) cc_final: 0.7620 (mmt) REVERT: A 669 ARG cc_start: 0.8780 (ttp80) cc_final: 0.8185 (ttp-110) REVERT: A 686 LEU cc_start: 0.8936 (mp) cc_final: 0.8614 (mp) REVERT: A 736 TRP cc_start: 0.7725 (OUTLIER) cc_final: 0.6330 (m100) outliers start: 20 outliers final: 15 residues processed: 108 average time/residue: 0.0692 time to fit residues: 10.0460 Evaluate side-chains 111 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 16 optimal weight: 0.0040 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 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 = 0.3728 r_free = 0.3728 target = 0.132211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097587 restraints weight = 9100.037| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.07 r_work: 0.3130 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5760 Z= 0.124 Angle : 0.645 11.510 7842 Z= 0.311 Chirality : 0.042 0.189 932 Planarity : 0.004 0.053 990 Dihedral : 4.826 56.634 826 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.17 % Allowed : 23.04 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.34), residues: 730 helix: 1.86 (0.25), residues: 473 sheet: -2.21 (0.73), residues: 43 loop : -1.53 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 653 TYR 0.018 0.001 TYR A 10 PHE 0.009 0.001 PHE A 12 TRP 0.005 0.001 TRP A 108 HIS 0.001 0.000 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 5760) covalent geometry : angle 0.64509 ( 7842) hydrogen bonds : bond 0.04032 ( 376) hydrogen bonds : angle 4.71279 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.205 Fit side-chains REVERT: A 13 ARG cc_start: 0.7680 (pmt170) cc_final: 0.7479 (ptp90) REVERT: A 284 MET cc_start: 0.6880 (mtp) cc_final: 0.6546 (mtp) REVERT: A 346 ASP cc_start: 0.8299 (m-30) cc_final: 0.7384 (t0) REVERT: A 390 TRP cc_start: 0.7401 (OUTLIER) cc_final: 0.6747 (m-90) REVERT: A 398 MET cc_start: 0.8464 (tpp) cc_final: 0.7973 (tmm) REVERT: A 444 GLN cc_start: 0.8739 (tp40) cc_final: 0.8499 (tt0) REVERT: A 540 HIS cc_start: 0.7997 (t70) cc_final: 0.7411 (t-90) REVERT: A 625 GLN cc_start: 0.8768 (pt0) cc_final: 0.8222 (pm20) REVERT: A 662 MET cc_start: 0.7997 (mpp) cc_final: 0.7666 (mmt) REVERT: A 669 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8174 (ttp-110) REVERT: A 686 LEU cc_start: 0.8910 (mp) cc_final: 0.8603 (mp) REVERT: A 736 TRP cc_start: 0.7596 (OUTLIER) cc_final: 0.6285 (m100) outliers start: 19 outliers final: 15 residues processed: 108 average time/residue: 0.0617 time to fit residues: 9.1458 Evaluate side-chains 111 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 39 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 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 = 0.3737 r_free = 0.3737 target = 0.130840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.097758 restraints weight = 8920.403| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.74 r_work: 0.3129 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5760 Z= 0.133 Angle : 0.658 11.808 7842 Z= 0.315 Chirality : 0.042 0.190 932 Planarity : 0.004 0.040 990 Dihedral : 4.797 56.211 826 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.01 % Allowed : 24.21 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.34), residues: 730 helix: 1.84 (0.25), residues: 474 sheet: -2.10 (0.74), residues: 43 loop : -1.44 (0.46), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.018 0.001 TYR A 10 PHE 0.020 0.001 PHE A 260 TRP 0.005 0.001 TRP A 741 HIS 0.001 0.000 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 5760) covalent geometry : angle 0.65772 ( 7842) hydrogen bonds : bond 0.04169 ( 376) hydrogen bonds : angle 4.71826 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.200 Fit side-chains REVERT: A 284 MET cc_start: 0.6963 (mtp) cc_final: 0.6642 (mtp) REVERT: A 346 ASP cc_start: 0.8226 (m-30) cc_final: 0.7367 (t0) REVERT: A 390 TRP cc_start: 0.7527 (OUTLIER) cc_final: 0.6843 (m-90) REVERT: A 398 MET cc_start: 0.8417 (tpp) cc_final: 0.7966 (mmm) REVERT: A 444 GLN cc_start: 0.8778 (tp40) cc_final: 0.8576 (tt0) REVERT: A 540 HIS cc_start: 0.7904 (t70) cc_final: 0.7367 (t-90) REVERT: A 546 VAL cc_start: 0.8996 (m) cc_final: 0.8703 (t) REVERT: A 625 GLN cc_start: 0.8725 (pt0) cc_final: 0.8259 (pm20) REVERT: A 662 MET cc_start: 0.8122 (mpp) cc_final: 0.7836 (mmt) REVERT: A 669 ARG cc_start: 0.8837 (ttp80) cc_final: 0.8248 (ttp-110) REVERT: A 736 TRP cc_start: 0.7531 (OUTLIER) cc_final: 0.6186 (m100) outliers start: 18 outliers final: 15 residues processed: 106 average time/residue: 0.0673 time to fit residues: 9.6600 Evaluate side-chains 109 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 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 = 0.3744 r_free = 0.3744 target = 0.132273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.098605 restraints weight = 8674.296| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.86 r_work: 0.3137 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5760 Z= 0.132 Angle : 0.654 11.548 7842 Z= 0.316 Chirality : 0.042 0.178 932 Planarity : 0.004 0.052 990 Dihedral : 4.807 56.463 826 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.01 % Allowed : 24.37 % Favored : 72.62 % 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: 1.04 (0.34), residues: 730 helix: 1.85 (0.25), residues: 473 sheet: -2.02 (0.75), residues: 43 loop : -1.38 (0.46), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.019 0.001 TYR A 10 PHE 0.008 0.001 PHE A 12 TRP 0.005 0.001 TRP A 741 HIS 0.001 0.000 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 5760) covalent geometry : angle 0.65440 ( 7842) hydrogen bonds : bond 0.04144 ( 376) hydrogen bonds : angle 4.70430 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1295.34 seconds wall clock time: 22 minutes 43.29 seconds (1363.29 seconds total)