Starting phenix.real_space_refine on Mon Jul 28 01:11:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wnx_32634/07_2025/7wnx_32634.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wnx_32634/07_2025/7wnx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wnx_32634/07_2025/7wnx_32634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wnx_32634/07_2025/7wnx_32634.map" model { file = "/net/cci-nas-00/data/ceres_data/7wnx_32634/07_2025/7wnx_32634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wnx_32634/07_2025/7wnx_32634.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.77, per 1000 atoms: 0.67 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: 1.43 Conformation dependent library (CDL) restraints added in 774.9 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: 0.52 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: 1.54 Time building geometry restraints manager: 1.66 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.940 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.130 ------------------------------------------------------------------------------- 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 : 8.77 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP A 736 HIS 0.001 0.000 HIS A 132 PHE 0.015 0.001 PHE A 12 TYR 0.013 0.001 TYR A 10 ARG 0.002 0.000 ARG A 288 Details of bonding type rmsd hydrogen bonds : bond 0.12278 ( 376) hydrogen bonds : angle 5.69542 ( 1086) covalent geometry : bond 0.00432 ( 5760) covalent geometry : angle 0.67650 ( 7842) *********************** 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 : 0.582 Fit side-chains REVERT: A 13 ARG cc_start: 0.7708 (pmt170) cc_final: 0.7409 (ptp90) REVERT: A 284 MET cc_start: 0.6768 (mtp) cc_final: 0.6482 (mtp) REVERT: A 444 GLN cc_start: 0.8687 (tp40) cc_final: 0.8472 (tt0) REVERT: A 620 MET cc_start: 0.8322 (mmm) cc_final: 0.8085 (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: 0.1866 time to fit residues: 29.3842 Evaluate side-chains 89 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 61 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 HIS ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.128449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.094309 restraints weight = 8858.571| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.86 r_work: 0.3082 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5760 Z= 0.148 Angle : 0.615 7.142 7842 Z= 0.316 Chirality : 0.041 0.127 932 Planarity : 0.005 0.053 990 Dihedral : 5.594 54.201 827 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.34 % Allowed : 14.52 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.32), residues: 730 helix: 0.86 (0.25), residues: 469 sheet: -3.08 (0.67), residues: 43 loop : -2.46 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.002 0.001 HIS A 540 PHE 0.017 0.001 PHE A 722 TYR 0.013 0.001 TYR A 10 ARG 0.003 0.000 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.04833 ( 376) hydrogen bonds : angle 4.95570 ( 1086) covalent geometry : bond 0.00330 ( 5760) covalent geometry : angle 0.61502 ( 7842) *********************** 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 112 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.784 Fit side-chains REVERT: A 13 ARG cc_start: 0.7655 (pmt170) cc_final: 0.7168 (ptp90) REVERT: A 191 VAL cc_start: 0.7908 (p) cc_final: 0.7706 (p) REVERT: A 284 MET cc_start: 0.7050 (mtp) cc_final: 0.6761 (mtp) REVERT: A 444 GLN cc_start: 0.8817 (tp40) cc_final: 0.8489 (tt0) REVERT: A 499 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8417 (mtpp) REVERT: A 620 MET cc_start: 0.8717 (mmm) cc_final: 0.8475 (mmm) REVERT: A 662 MET cc_start: 0.8068 (mpp) cc_final: 0.7720 (mpp) REVERT: A 669 ARG cc_start: 0.8863 (ttp80) cc_final: 0.8312 (ttm110) REVERT: A 736 TRP cc_start: 0.8126 (OUTLIER) cc_final: 0.6333 (m100) outliers start: 14 outliers final: 8 residues processed: 109 average time/residue: 0.2009 time to fit residues: 29.0704 Evaluate side-chains 94 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 586 VAL 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 58 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3656 r_free = 0.3656 target = 0.125994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.090815 restraints weight = 9107.592| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.03 r_work: 0.3023 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5760 Z= 0.196 Angle : 0.651 8.704 7842 Z= 0.328 Chirality : 0.042 0.139 932 Planarity : 0.005 0.053 990 Dihedral : 5.648 56.115 827 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 3.67 % Allowed : 19.03 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.33), residues: 730 helix: 1.23 (0.25), residues: 473 sheet: -2.90 (0.68), residues: 43 loop : -2.27 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 498 HIS 0.002 0.001 HIS A 540 PHE 0.026 0.002 PHE A 202 TYR 0.014 0.001 TYR A 10 ARG 0.003 0.000 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.05219 ( 376) hydrogen bonds : angle 4.98823 ( 1086) covalent geometry : bond 0.00459 ( 5760) covalent geometry : angle 0.65081 ( 7842) *********************** 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 109 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.603 Fit side-chains REVERT: A 13 ARG cc_start: 0.7731 (pmt170) cc_final: 0.7303 (ptp90) REVERT: A 284 MET cc_start: 0.6989 (mtp) cc_final: 0.6703 (mtp) REVERT: A 390 TRP cc_start: 0.7306 (OUTLIER) cc_final: 0.6662 (m-90) REVERT: A 398 MET cc_start: 0.8482 (tpp) cc_final: 0.8069 (tmm) REVERT: A 444 GLN cc_start: 0.8779 (tp40) cc_final: 0.8442 (tt0) REVERT: A 523 ARG cc_start: 0.8523 (tpt-90) cc_final: 0.8251 (tpt-90) REVERT: A 558 HIS cc_start: 0.7529 (t70) cc_final: 0.7196 (t-90) REVERT: A 620 MET cc_start: 0.8758 (mmm) cc_final: 0.8481 (mmm) REVERT: A 660 ARG cc_start: 0.8275 (mpp80) cc_final: 0.8042 (mpp80) REVERT: A 662 MET cc_start: 0.8083 (mpp) cc_final: 0.7663 (mpp) REVERT: A 669 ARG cc_start: 0.8790 (ttp80) cc_final: 0.8211 (ttm110) REVERT: A 736 TRP cc_start: 0.8024 (OUTLIER) cc_final: 0.6609 (m100) outliers start: 22 outliers final: 15 residues processed: 102 average time/residue: 0.1629 time to fit residues: 22.1637 Evaluate side-chains 100 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 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 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 585 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 694 VAL 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 61 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 0.0670 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.128723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.093743 restraints weight = 9203.092| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.05 r_work: 0.3067 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5760 Z= 0.140 Angle : 0.603 7.337 7842 Z= 0.304 Chirality : 0.040 0.129 932 Planarity : 0.004 0.050 990 Dihedral : 5.113 54.761 826 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.01 % Allowed : 20.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.33), residues: 730 helix: 1.46 (0.25), residues: 479 sheet: -2.76 (0.70), residues: 43 loop : -2.10 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.001 0.001 HIS A 239 PHE 0.012 0.001 PHE A 12 TYR 0.013 0.001 TYR A 10 ARG 0.002 0.000 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.04579 ( 376) hydrogen bonds : angle 4.82823 ( 1086) covalent geometry : bond 0.00309 ( 5760) covalent geometry : angle 0.60331 ( 7842) *********************** 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 110 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.701 Fit side-chains REVERT: A 13 ARG cc_start: 0.7623 (pmt170) cc_final: 0.7299 (ptp90) REVERT: A 191 VAL cc_start: 0.7756 (OUTLIER) cc_final: 0.7547 (p) REVERT: A 284 MET cc_start: 0.7039 (mtp) cc_final: 0.6738 (mtp) REVERT: A 346 ASP cc_start: 0.8309 (m-30) cc_final: 0.7359 (t0) REVERT: A 390 TRP cc_start: 0.7375 (OUTLIER) cc_final: 0.6771 (m-90) REVERT: A 398 MET cc_start: 0.8410 (tpp) cc_final: 0.8031 (tmm) REVERT: A 444 GLN cc_start: 0.8784 (tp40) cc_final: 0.8474 (tt0) REVERT: A 620 MET cc_start: 0.8760 (mmm) cc_final: 0.8501 (mmm) REVERT: A 669 ARG cc_start: 0.8807 (ttp80) cc_final: 0.8246 (ttm110) REVERT: A 736 TRP cc_start: 0.7869 (OUTLIER) cc_final: 0.6502 (m100) outliers start: 18 outliers final: 8 residues processed: 105 average time/residue: 0.1993 time to fit residues: 27.6466 Evaluate side-chains 94 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 259 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 38 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.129097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094277 restraints weight = 9076.037| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.04 r_work: 0.3076 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1889 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= 0.136 Angle : 0.605 7.487 7842 Z= 0.303 Chirality : 0.041 0.159 932 Planarity : 0.004 0.037 990 Dihedral : 5.070 55.590 826 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 3.34 % Allowed : 22.20 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.33), residues: 730 helix: 1.64 (0.25), residues: 476 sheet: -2.66 (0.70), residues: 43 loop : -1.94 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.001 0.001 HIS A 132 PHE 0.013 0.001 PHE A 12 TYR 0.015 0.001 TYR A 10 ARG 0.003 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 376) hydrogen bonds : angle 4.78818 ( 1086) covalent geometry : bond 0.00299 ( 5760) covalent geometry : angle 0.60473 ( 7842) *********************** 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 114 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.566 Fit side-chains REVERT: A 13 ARG cc_start: 0.7581 (pmt170) cc_final: 0.7235 (ptp90) REVERT: A 284 MET cc_start: 0.6950 (mtp) cc_final: 0.6634 (mtp) REVERT: A 346 ASP cc_start: 0.8321 (m-30) cc_final: 0.7360 (t0) REVERT: A 390 TRP cc_start: 0.7268 (OUTLIER) cc_final: 0.6636 (m-90) REVERT: A 398 MET cc_start: 0.8421 (tpp) cc_final: 0.8023 (tmm) REVERT: A 444 GLN cc_start: 0.8752 (tp40) cc_final: 0.8446 (tt0) REVERT: A 620 MET cc_start: 0.8766 (mmm) cc_final: 0.8478 (mmm) REVERT: A 669 ARG cc_start: 0.8754 (ttp80) cc_final: 0.8132 (ttp-110) REVERT: A 733 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8146 (p0) REVERT: A 736 TRP cc_start: 0.7842 (OUTLIER) cc_final: 0.6452 (m100) outliers start: 20 outliers final: 15 residues processed: 109 average time/residue: 0.2358 time to fit residues: 33.9290 Evaluate side-chains 105 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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 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 733 ASP 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 62 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.131173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.096531 restraints weight = 8895.580| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.04 r_work: 0.3111 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2079 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= 0.123 Angle : 0.587 6.191 7842 Z= 0.293 Chirality : 0.040 0.167 932 Planarity : 0.004 0.038 990 Dihedral : 4.944 57.032 826 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.01 % Allowed : 21.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.34), residues: 730 helix: 1.79 (0.25), residues: 477 sheet: -2.54 (0.71), residues: 43 loop : -1.76 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.001 0.000 HIS A 132 PHE 0.008 0.001 PHE A 12 TYR 0.015 0.001 TYR A 10 ARG 0.003 0.000 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.04180 ( 376) hydrogen bonds : angle 4.70928 ( 1086) covalent geometry : bond 0.00261 ( 5760) covalent geometry : angle 0.58680 ( 7842) *********************** 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 120 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.584 Fit side-chains REVERT: A 13 ARG cc_start: 0.7620 (pmt170) cc_final: 0.7348 (ptp90) REVERT: A 284 MET cc_start: 0.6917 (mtp) cc_final: 0.6585 (mtp) REVERT: A 346 ASP cc_start: 0.8326 (m-30) cc_final: 0.7364 (t0) REVERT: A 390 TRP cc_start: 0.7402 (OUTLIER) cc_final: 0.6678 (m-90) REVERT: A 398 MET cc_start: 0.8278 (tpp) cc_final: 0.7891 (tmm) REVERT: A 444 GLN cc_start: 0.8750 (tp40) cc_final: 0.8509 (tt0) REVERT: A 540 HIS cc_start: 0.8021 (t70) cc_final: 0.7413 (t-90) REVERT: A 620 MET cc_start: 0.8716 (mmm) cc_final: 0.8452 (mmm) REVERT: A 625 GLN cc_start: 0.8788 (pt0) cc_final: 0.8222 (pm20) REVERT: A 669 ARG cc_start: 0.8788 (ttp80) cc_final: 0.8204 (ttp-110) REVERT: A 686 LEU cc_start: 0.8931 (mp) cc_final: 0.8661 (mp) REVERT: A 721 MET cc_start: 0.7957 (ptp) cc_final: 0.7550 (ptm) REVERT: A 736 TRP cc_start: 0.7729 (OUTLIER) cc_final: 0.6269 (m100) outliers start: 24 outliers final: 13 residues processed: 114 average time/residue: 0.1653 time to fit residues: 25.1247 Evaluate side-chains 108 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 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 736 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.130328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.095787 restraints weight = 9071.506| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.94 r_work: 0.3109 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2175 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= 0.130 Angle : 0.615 11.248 7842 Z= 0.304 Chirality : 0.041 0.191 932 Planarity : 0.004 0.059 990 Dihedral : 4.932 57.272 826 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.34 % Allowed : 22.04 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.34), residues: 730 helix: 1.81 (0.25), residues: 476 sheet: -2.45 (0.71), residues: 43 loop : -1.72 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 741 HIS 0.001 0.000 HIS A 132 PHE 0.016 0.001 PHE A 260 TYR 0.015 0.001 TYR A 10 ARG 0.003 0.000 ARG A 478 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 376) hydrogen bonds : angle 4.76100 ( 1086) covalent geometry : bond 0.00283 ( 5760) covalent geometry : angle 0.61531 ( 7842) *********************** 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 122 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.910 Fit side-chains REVERT: A 284 MET cc_start: 0.6949 (mtp) cc_final: 0.6612 (mtp) REVERT: A 346 ASP cc_start: 0.8267 (m-30) cc_final: 0.7360 (t0) REVERT: A 390 TRP cc_start: 0.7450 (OUTLIER) cc_final: 0.6652 (m-90) REVERT: A 398 MET cc_start: 0.8227 (tpp) cc_final: 0.7876 (tmm) REVERT: A 444 GLN cc_start: 0.8774 (tp40) cc_final: 0.8550 (tt0) REVERT: A 540 HIS cc_start: 0.7960 (t70) cc_final: 0.7377 (t-90) REVERT: A 620 MET cc_start: 0.8665 (mmm) cc_final: 0.8438 (mmm) REVERT: A 625 GLN cc_start: 0.8733 (pt0) cc_final: 0.8247 (pm20) REVERT: A 662 MET cc_start: 0.8034 (mpp) cc_final: 0.7704 (mmt) REVERT: A 669 ARG cc_start: 0.8803 (ttp80) cc_final: 0.8209 (ttp-110) REVERT: A 686 LEU cc_start: 0.8959 (mp) cc_final: 0.8678 (mp) REVERT: A 721 MET cc_start: 0.7977 (ptp) cc_final: 0.7570 (ptm) REVERT: A 736 TRP cc_start: 0.7660 (OUTLIER) cc_final: 0.6179 (m100) outliers start: 26 outliers final: 20 residues processed: 113 average time/residue: 0.1534 time to fit residues: 23.7095 Evaluate side-chains 116 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 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 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 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 706 PHE 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 13 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.131170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.096893 restraints weight = 8762.418| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.87 r_work: 0.3130 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2299 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= 0.125 Angle : 0.620 11.614 7842 Z= 0.303 Chirality : 0.041 0.176 932 Planarity : 0.004 0.040 990 Dihedral : 4.899 57.879 826 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.84 % Allowed : 22.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.34), residues: 730 helix: 1.85 (0.25), residues: 472 sheet: -2.27 (0.72), residues: 43 loop : -1.60 (0.45), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.001 0.000 HIS A 132 PHE 0.017 0.001 PHE A 260 TYR 0.016 0.001 TYR A 10 ARG 0.003 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 376) hydrogen bonds : angle 4.76154 ( 1086) covalent geometry : bond 0.00265 ( 5760) covalent geometry : angle 0.62026 ( 7842) *********************** 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 117 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.753 Fit side-chains REVERT: A 346 ASP cc_start: 0.8264 (m-30) cc_final: 0.7372 (t0) REVERT: A 390 TRP cc_start: 0.7433 (OUTLIER) cc_final: 0.6658 (m-90) REVERT: A 398 MET cc_start: 0.8207 (tpp) cc_final: 0.7852 (tmm) REVERT: A 444 GLN cc_start: 0.8728 (tp40) cc_final: 0.8509 (tt0) REVERT: A 540 HIS cc_start: 0.7987 (t70) cc_final: 0.7386 (t-90) REVERT: A 546 VAL cc_start: 0.8945 (m) cc_final: 0.8649 (t) REVERT: A 625 GLN cc_start: 0.8771 (pt0) cc_final: 0.8240 (pm20) REVERT: A 669 ARG cc_start: 0.8781 (ttp80) cc_final: 0.8198 (ttp-110) REVERT: A 686 LEU cc_start: 0.8940 (mp) cc_final: 0.8658 (mp) REVERT: A 721 MET cc_start: 0.7929 (ptp) cc_final: 0.7544 (ptm) REVERT: A 736 TRP cc_start: 0.7562 (OUTLIER) cc_final: 0.6087 (m100) outliers start: 23 outliers final: 16 residues processed: 108 average time/residue: 0.1960 time to fit residues: 29.9970 Evaluate side-chains 109 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 323 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.0670 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.133267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.099067 restraints weight = 8677.643| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.88 r_work: 0.3156 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2420 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 : 0.635 10.703 7842 Z= 0.307 Chirality : 0.041 0.181 932 Planarity : 0.004 0.055 990 Dihedral : 4.875 58.387 826 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.01 % Allowed : 23.71 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.34), residues: 730 helix: 1.86 (0.25), residues: 475 sheet: -2.10 (0.73), residues: 43 loop : -1.60 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 741 HIS 0.001 0.000 HIS A 239 PHE 0.019 0.001 PHE A 260 TYR 0.016 0.001 TYR A 10 ARG 0.003 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 376) hydrogen bonds : angle 4.74225 ( 1086) covalent geometry : bond 0.00264 ( 5760) covalent geometry : angle 0.63454 ( 7842) *********************** 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 115 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.638 Fit side-chains REVERT: A 284 MET cc_start: 0.6821 (ttm) cc_final: 0.6413 (mtp) REVERT: A 346 ASP cc_start: 0.8265 (m-30) cc_final: 0.7365 (t0) REVERT: A 390 TRP cc_start: 0.7340 (OUTLIER) cc_final: 0.6686 (m-90) REVERT: A 398 MET cc_start: 0.8248 (tpp) cc_final: 0.7886 (tmm) REVERT: A 444 GLN cc_start: 0.8728 (tp40) cc_final: 0.8518 (tt0) REVERT: A 468 PRO cc_start: 0.8702 (Cg_exo) cc_final: 0.8285 (Cg_endo) REVERT: A 540 HIS cc_start: 0.8072 (t70) cc_final: 0.7436 (t-90) REVERT: A 546 VAL cc_start: 0.8935 (m) cc_final: 0.8642 (t) REVERT: A 625 GLN cc_start: 0.8797 (pt0) cc_final: 0.8217 (pm20) REVERT: A 669 ARG cc_start: 0.8761 (ttp80) cc_final: 0.8175 (ttp-110) REVERT: A 686 LEU cc_start: 0.8891 (mp) cc_final: 0.8597 (mp) REVERT: A 736 TRP cc_start: 0.7497 (OUTLIER) cc_final: 0.6029 (m100) outliers start: 18 outliers final: 16 residues processed: 110 average time/residue: 0.1850 time to fit residues: 26.8850 Evaluate side-chains 108 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 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 323 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 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 54 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 0.0070 overall best weight: 1.1800 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.132300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.098621 restraints weight = 8802.106| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.77 r_work: 0.3142 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2448 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= 0.136 Angle : 0.667 12.143 7842 Z= 0.320 Chirality : 0.042 0.215 932 Planarity : 0.004 0.058 990 Dihedral : 4.894 58.172 826 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.01 % Allowed : 24.54 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.34), residues: 730 helix: 1.83 (0.25), residues: 473 sheet: -2.01 (0.75), residues: 43 loop : -1.49 (0.46), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 5 HIS 0.001 0.000 HIS A 239 PHE 0.017 0.001 PHE A 260 TYR 0.017 0.001 TYR A 10 ARG 0.003 0.000 ARG A 7 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 376) hydrogen bonds : angle 4.74639 ( 1086) covalent geometry : bond 0.00303 ( 5760) covalent geometry : angle 0.66725 ( 7842) ********************** 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 111 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.637 Fit side-chains REVERT: A 13 ARG cc_start: 0.7652 (pmt170) cc_final: 0.7370 (ptp90) REVERT: A 284 MET cc_start: 0.6825 (ttm) cc_final: 0.6402 (mtp) REVERT: A 346 ASP cc_start: 0.8309 (m-30) cc_final: 0.7350 (t0) REVERT: A 390 TRP cc_start: 0.7366 (OUTLIER) cc_final: 0.6761 (m-90) REVERT: A 398 MET cc_start: 0.8331 (tpp) cc_final: 0.7961 (tmm) REVERT: A 444 GLN cc_start: 0.8732 (tp40) cc_final: 0.8530 (tt0) REVERT: A 540 HIS cc_start: 0.8039 (t70) cc_final: 0.7440 (t-90) REVERT: A 546 VAL cc_start: 0.8953 (m) cc_final: 0.8674 (t) REVERT: A 625 GLN cc_start: 0.8795 (pt0) cc_final: 0.8205 (pm20) REVERT: A 669 ARG cc_start: 0.8760 (ttp80) cc_final: 0.8165 (ttp-110) REVERT: A 686 LEU cc_start: 0.8900 (mp) cc_final: 0.8621 (mp) REVERT: A 736 TRP cc_start: 0.7492 (OUTLIER) cc_final: 0.6007 (m100) outliers start: 18 outliers final: 15 residues processed: 106 average time/residue: 0.1575 time to fit residues: 22.5797 Evaluate side-chains 110 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 323 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 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 55 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.133160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.099254 restraints weight = 8663.071| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.85 r_work: 0.3158 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5760 Z= 0.128 Angle : 0.660 12.104 7842 Z= 0.316 Chirality : 0.042 0.193 932 Planarity : 0.004 0.039 990 Dihedral : 4.843 58.567 826 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.01 % Allowed : 24.54 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.34), residues: 730 helix: 1.88 (0.25), residues: 475 sheet: -1.98 (0.74), residues: 43 loop : -1.52 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 741 HIS 0.002 0.000 HIS A 239 PHE 0.016 0.001 PHE A 260 TYR 0.016 0.001 TYR A 10 ARG 0.002 0.000 ARG A 7 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 376) hydrogen bonds : angle 4.71266 ( 1086) covalent geometry : bond 0.00280 ( 5760) covalent geometry : angle 0.65970 ( 7842) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3313.11 seconds wall clock time: 59 minutes 16.67 seconds (3556.67 seconds total)