Starting phenix.real_space_refine on Tue Mar 3 11:33:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wlc_32581/03_2026/7wlc_32581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wlc_32581/03_2026/7wlc_32581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wlc_32581/03_2026/7wlc_32581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wlc_32581/03_2026/7wlc_32581.map" model { file = "/net/cci-nas-00/data/ceres_data/7wlc_32581/03_2026/7wlc_32581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wlc_32581/03_2026/7wlc_32581.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2094 2.51 5 N 563 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s 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: 3307 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 187} Chain: "H" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 892 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 803 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 0.93, per 1000 atoms: 0.28 Number of scatterers: 3307 At special positions: 0 Unit cell: (53.04, 80.08, 95.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 636 8.00 N 563 7.00 C 2094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.20 Conformation dependent library (CDL) restraints added in 128.5 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 784 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 8.8% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'E' and resid 337 through 342 removed outlier: 3.781A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 386 through 389 removed outlier: 3.657A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 386 through 389' Processing helix chain 'E' and resid 405 through 411 removed outlier: 4.535A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA E 411 " --> pdb=" O ARG E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 removed outlier: 3.569A pdb=" N ASN E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.730A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'E' and resid 356 through 358 removed outlier: 3.730A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 391 through 392 removed outlier: 3.634A pdb=" N VAL E 524 " --> pdb=" O PHE E 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 453 through 454 Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.694A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.789A pdb=" N GLU H 10 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA H 118 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.625A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA9, first strand: chain 'L' and resid 18 through 23 100 hydrogen bonds defined for protein. 237 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: 0.50 Time building geometry restraints manager: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1071 1.34 - 1.47: 889 1.47 - 1.59: 1416 1.59 - 1.71: 0 1.71 - 1.84: 16 Bond restraints: 3392 Sorted by residual: bond pdb=" CB LYS H 13 " pdb=" CG LYS H 13 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CB ASN E 448 " pdb=" CG ASN E 448 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" N GLY H 112 " pdb=" CA GLY H 112 " ideal model delta sigma weight residual 1.444 1.454 -0.010 9.60e-03 1.09e+04 9.95e-01 bond pdb=" C ASN E 331 " pdb=" N ILE E 332 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.40e-02 5.10e+03 9.85e-01 bond pdb=" CG LYS H 13 " pdb=" CD LYS H 13 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.82e-01 ... (remaining 3387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 4508 1.92 - 3.83: 86 3.83 - 5.75: 13 5.75 - 7.67: 5 7.67 - 9.59: 2 Bond angle restraints: 4614 Sorted by residual: angle pdb=" C ASN E 331 " pdb=" N ILE E 332 " pdb=" CA ILE E 332 " ideal model delta sigma weight residual 121.70 128.16 -6.46 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA MET H 81 " pdb=" CB MET H 81 " pdb=" CG MET H 81 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CB LYS H 13 " pdb=" CG LYS H 13 " pdb=" CD LYS H 13 " ideal model delta sigma weight residual 111.30 119.20 -7.90 2.30e+00 1.89e-01 1.18e+01 angle pdb=" CB MET H 81 " pdb=" CG MET H 81 " pdb=" SD MET H 81 " ideal model delta sigma weight residual 112.70 103.11 9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CA TRP H 111 " pdb=" CB TRP H 111 " pdb=" CG TRP H 111 " ideal model delta sigma weight residual 113.60 119.66 -6.06 1.90e+00 2.77e-01 1.02e+01 ... (remaining 4609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 1779 15.37 - 30.74: 175 30.74 - 46.11: 29 46.11 - 61.48: 13 61.48 - 76.85: 8 Dihedral angle restraints: 2004 sinusoidal: 768 harmonic: 1236 Sorted by residual: dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual 93.00 28.64 64.36 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS E 336 " pdb=" SG CYS E 336 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual 93.00 34.26 58.74 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CA MET H 81 " pdb=" C MET H 81 " pdb=" N GLU H 82 " pdb=" CA GLU H 82 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 2001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 244 0.028 - 0.056: 160 0.056 - 0.084: 57 0.084 - 0.111: 25 0.111 - 0.139: 11 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA ILE H 70 " pdb=" N ILE H 70 " pdb=" C ILE H 70 " pdb=" CB ILE H 70 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA PRO E 373 " pdb=" N PRO E 373 " pdb=" C PRO E 373 " pdb=" CB PRO E 373 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE L 76 " pdb=" N ILE L 76 " pdb=" C ILE L 76 " pdb=" CB ILE L 76 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 494 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 59 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO L 60 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 111 " -0.015 2.00e-02 2.50e+03 9.52e-03 2.27e+00 pdb=" CG TRP H 111 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP H 111 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP H 111 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 111 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 111 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 111 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 111 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 111 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 111 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS E 336 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO E 337 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 337 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 337 " 0.019 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 234 2.74 - 3.28: 3348 3.28 - 3.82: 5244 3.82 - 4.36: 5995 4.36 - 4.90: 10460 Nonbonded interactions: 25281 Sorted by model distance: nonbonded pdb=" O ASN E 448 " pdb=" OG SER E 494 " model vdw 2.198 3.040 nonbonded pdb=" NZ LYS H 23 " pdb=" O THR H 76 " model vdw 2.242 3.120 nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 115 " model vdw 2.263 3.040 nonbonded pdb=" O TYR H 108 " pdb=" OH TYR L 37 " model vdw 2.264 3.040 nonbonded pdb=" O ARG H 67 " pdb=" OG SER H 84 " model vdw 2.271 3.040 ... (remaining 25276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.020 Find NCS groups from input model: 0.010 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:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3398 Z= 0.139 Angle : 0.705 9.586 4626 Z= 0.380 Chirality : 0.044 0.139 497 Planarity : 0.005 0.039 601 Dihedral : 13.708 76.851 1202 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.35 (0.42), residues: 424 helix: -3.38 (0.98), residues: 18 sheet: 0.25 (0.50), residues: 131 loop : -1.37 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 346 TYR 0.018 0.001 TYR E 351 PHE 0.021 0.002 PHE E 497 TRP 0.024 0.002 TRP H 111 HIS 0.001 0.000 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3392) covalent geometry : angle 0.70106 ( 4614) SS BOND : bond 0.00423 ( 6) SS BOND : angle 1.58104 ( 12) hydrogen bonds : bond 0.13124 ( 93) hydrogen bonds : angle 8.67802 ( 237) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 392 PHE cc_start: 0.8997 (m-80) cc_final: 0.8779 (m-80) REVERT: E 467 ASP cc_start: 0.7961 (t70) cc_final: 0.7735 (t0) REVERT: H 29 PHE cc_start: 0.7613 (t80) cc_final: 0.7264 (t80) REVERT: H 67 ARG cc_start: 0.8905 (ptp-170) cc_final: 0.8544 (ttp-110) REVERT: L 39 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7662 (tp-100) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0715 time to fit residues: 8.3798 Evaluate side-chains 80 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 40.0000 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 50.0000 chunk 31 optimal weight: 50.0000 chunk 25 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 50.0000 chunk 22 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 overall best weight: 12.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN H 6 GLN H 110 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.122757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.093177 restraints weight = 9145.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.096028 restraints weight = 5373.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.097872 restraints weight = 3744.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.099071 restraints weight = 2930.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.099688 restraints weight = 2485.621| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3398 Z= 0.239 Angle : 0.764 10.495 4626 Z= 0.402 Chirality : 0.048 0.142 497 Planarity : 0.005 0.042 601 Dihedral : 5.966 19.648 471 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 2.79 % Allowed : 15.88 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.44 (0.41), residues: 424 helix: -3.44 (1.30), residues: 12 sheet: 0.03 (0.47), residues: 140 loop : -1.43 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 17 TYR 0.018 0.002 TYR E 449 PHE 0.029 0.003 PHE E 429 TRP 0.021 0.003 TRP H 111 HIS 0.002 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 3392) covalent geometry : angle 0.76087 ( 4614) SS BOND : bond 0.00315 ( 6) SS BOND : angle 1.53442 ( 12) hydrogen bonds : bond 0.04065 ( 93) hydrogen bonds : angle 7.16535 ( 237) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 346 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7857 (mtp85) REVERT: E 467 ASP cc_start: 0.7909 (t70) cc_final: 0.7701 (t0) REVERT: H 29 PHE cc_start: 0.8045 (t80) cc_final: 0.7532 (t80) REVERT: H 38 ARG cc_start: 0.8421 (ptt180) cc_final: 0.8171 (ptt180) REVERT: H 48 MET cc_start: 0.8350 (mmp) cc_final: 0.8041 (tpt) REVERT: H 67 ARG cc_start: 0.8799 (ptp-170) cc_final: 0.8587 (ttp-110) REVERT: L 39 GLN cc_start: 0.7976 (tp-100) cc_final: 0.7735 (tp-100) REVERT: L 93 ASP cc_start: 0.8017 (t0) cc_final: 0.7787 (t0) outliers start: 10 outliers final: 4 residues processed: 90 average time/residue: 0.0868 time to fit residues: 9.1088 Evaluate side-chains 81 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 108 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 40.0000 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 50.0000 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 31 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 24 optimal weight: 50.0000 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 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 = 0.3964 r_free = 0.3964 target = 0.124092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.094777 restraints weight = 9080.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.097632 restraints weight = 5326.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.099518 restraints weight = 3730.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.100746 restraints weight = 2914.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.101375 restraints weight = 2461.973| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3398 Z= 0.158 Angle : 0.711 9.589 4626 Z= 0.362 Chirality : 0.047 0.140 497 Planarity : 0.005 0.041 601 Dihedral : 5.694 19.169 471 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.23 % Allowed : 16.43 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.39 (0.41), residues: 424 helix: -3.14 (1.12), residues: 18 sheet: 0.03 (0.46), residues: 140 loop : -1.34 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 17 TYR 0.012 0.002 TYR E 449 PHE 0.016 0.002 PHE E 429 TRP 0.022 0.002 TRP H 111 HIS 0.006 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 3392) covalent geometry : angle 0.70951 ( 4614) SS BOND : bond 0.00382 ( 6) SS BOND : angle 1.04260 ( 12) hydrogen bonds : bond 0.03405 ( 93) hydrogen bonds : angle 6.51586 ( 237) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 392 PHE cc_start: 0.9081 (m-80) cc_final: 0.8850 (m-80) REVERT: E 467 ASP cc_start: 0.7776 (t70) cc_final: 0.7552 (t0) REVERT: H 29 PHE cc_start: 0.7918 (t80) cc_final: 0.7401 (t80) REVERT: L 36 TRP cc_start: 0.7796 (m100) cc_final: 0.7437 (m100) REVERT: L 46 LYS cc_start: 0.9423 (tppp) cc_final: 0.9196 (tppp) outliers start: 8 outliers final: 6 residues processed: 87 average time/residue: 0.0833 time to fit residues: 8.5064 Evaluate side-chains 85 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 40.0000 chunk 28 optimal weight: 50.0000 chunk 40 optimal weight: 0.0060 chunk 32 optimal weight: 0.0020 chunk 26 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 overall best weight: 3.3608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 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 = 0.3992 r_free = 0.3992 target = 0.126349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.097120 restraints weight = 9178.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.099971 restraints weight = 5419.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.101883 restraints weight = 3809.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.103101 restraints weight = 2987.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.103874 restraints weight = 2535.639| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3398 Z= 0.124 Angle : 0.699 10.291 4626 Z= 0.353 Chirality : 0.046 0.136 497 Planarity : 0.004 0.042 601 Dihedral : 5.523 19.959 471 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.51 % Allowed : 19.78 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.20 (0.41), residues: 424 helix: -3.19 (1.05), residues: 18 sheet: 0.14 (0.48), residues: 135 loop : -1.16 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 17 TYR 0.015 0.001 TYR L 86 PHE 0.022 0.002 PHE H 64 TRP 0.027 0.002 TRP H 111 HIS 0.005 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3392) covalent geometry : angle 0.69716 ( 4614) SS BOND : bond 0.00584 ( 6) SS BOND : angle 1.19190 ( 12) hydrogen bonds : bond 0.03100 ( 93) hydrogen bonds : angle 6.20605 ( 237) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 474 GLN cc_start: 0.2699 (pp30) cc_final: 0.2361 (pp30) REVERT: H 29 PHE cc_start: 0.7852 (t80) cc_final: 0.7329 (t80) REVERT: H 48 MET cc_start: 0.8264 (mmp) cc_final: 0.7885 (tpp) REVERT: L 46 LYS cc_start: 0.9287 (tppp) cc_final: 0.9076 (tppp) outliers start: 9 outliers final: 6 residues processed: 88 average time/residue: 0.0876 time to fit residues: 9.0486 Evaluate side-chains 85 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 40.0000 chunk 30 optimal weight: 30.0000 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 21 optimal weight: 30.0000 chunk 41 optimal weight: 50.0000 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 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 = 0.3954 r_free = 0.3954 target = 0.123866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.094524 restraints weight = 9063.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.097396 restraints weight = 5327.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099252 restraints weight = 3726.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.100345 restraints weight = 2921.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.101194 restraints weight = 2496.110| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3398 Z= 0.169 Angle : 0.720 10.869 4626 Z= 0.366 Chirality : 0.046 0.140 497 Planarity : 0.005 0.043 601 Dihedral : 5.630 20.218 471 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.62 % Allowed : 20.61 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.41), residues: 424 helix: -3.41 (0.94), residues: 18 sheet: 0.04 (0.46), residues: 147 loop : -1.48 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 17 TYR 0.010 0.002 TYR E 495 PHE 0.018 0.002 PHE E 497 TRP 0.024 0.002 TRP H 111 HIS 0.004 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 3392) covalent geometry : angle 0.71654 ( 4614) SS BOND : bond 0.00323 ( 6) SS BOND : angle 1.47216 ( 12) hydrogen bonds : bond 0.03326 ( 93) hydrogen bonds : angle 6.27390 ( 237) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7924 (t80) cc_final: 0.7417 (t80) REVERT: H 48 MET cc_start: 0.8402 (mmp) cc_final: 0.7853 (tpp) REVERT: L 93 ASP cc_start: 0.8058 (t0) cc_final: 0.7832 (t0) outliers start: 13 outliers final: 8 residues processed: 84 average time/residue: 0.0791 time to fit residues: 7.8744 Evaluate side-chains 88 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 50.0000 chunk 18 optimal weight: 20.0000 chunk 39 optimal weight: 40.0000 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 17 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 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 = 0.3941 r_free = 0.3941 target = 0.123096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093462 restraints weight = 9091.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.096167 restraints weight = 5319.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.097972 restraints weight = 3759.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099157 restraints weight = 2955.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.099769 restraints weight = 2502.705| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3398 Z= 0.201 Angle : 0.747 11.883 4626 Z= 0.380 Chirality : 0.047 0.164 497 Planarity : 0.005 0.044 601 Dihedral : 5.763 21.483 471 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.34 % Allowed : 23.12 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.40), residues: 424 helix: -3.65 (0.85), residues: 18 sheet: -0.05 (0.47), residues: 141 loop : -1.47 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 17 TYR 0.011 0.002 TYR E 449 PHE 0.014 0.002 PHE E 338 TRP 0.027 0.003 TRP H 111 HIS 0.004 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 3392) covalent geometry : angle 0.74525 ( 4614) SS BOND : bond 0.00505 ( 6) SS BOND : angle 1.29678 ( 12) hydrogen bonds : bond 0.03363 ( 93) hydrogen bonds : angle 6.34764 ( 237) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 346 ARG cc_start: 0.8183 (mtp85) cc_final: 0.7774 (mtp85) REVERT: H 29 PHE cc_start: 0.7956 (t80) cc_final: 0.7397 (t80) REVERT: H 48 MET cc_start: 0.8457 (mmp) cc_final: 0.7711 (mmm) outliers start: 12 outliers final: 11 residues processed: 89 average time/residue: 0.0843 time to fit residues: 8.7662 Evaluate side-chains 90 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 37 optimal weight: 50.0000 chunk 6 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 12 optimal weight: 50.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 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 = 0.3945 r_free = 0.3945 target = 0.123538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.094055 restraints weight = 9184.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.096912 restraints weight = 5411.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.098787 restraints weight = 3796.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.099955 restraints weight = 2977.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.100495 restraints weight = 2526.889| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3398 Z= 0.164 Angle : 0.736 7.676 4626 Z= 0.374 Chirality : 0.046 0.147 497 Planarity : 0.005 0.045 601 Dihedral : 5.649 22.085 471 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.34 % Allowed : 25.07 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.55 (0.41), residues: 424 helix: -3.73 (0.78), residues: 18 sheet: -0.06 (0.47), residues: 140 loop : -1.42 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 17 TYR 0.016 0.002 TYR E 351 PHE 0.013 0.002 PHE E 374 TRP 0.027 0.003 TRP H 111 HIS 0.006 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 3392) covalent geometry : angle 0.73458 ( 4614) SS BOND : bond 0.00463 ( 6) SS BOND : angle 1.05065 ( 12) hydrogen bonds : bond 0.03140 ( 93) hydrogen bonds : angle 6.16403 ( 237) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 392 PHE cc_start: 0.9086 (m-80) cc_final: 0.8885 (m-10) REVERT: H 29 PHE cc_start: 0.7955 (t80) cc_final: 0.7384 (t80) REVERT: H 48 MET cc_start: 0.8381 (mmp) cc_final: 0.7775 (mmm) outliers start: 12 outliers final: 10 residues processed: 85 average time/residue: 0.0806 time to fit residues: 8.1207 Evaluate side-chains 90 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 30.0000 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 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 = 0.3957 r_free = 0.3957 target = 0.124159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.094693 restraints weight = 9018.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.097536 restraints weight = 5303.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.099383 restraints weight = 3711.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.100592 restraints weight = 2923.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.101220 restraints weight = 2478.796| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3398 Z= 0.148 Angle : 0.715 8.115 4626 Z= 0.360 Chirality : 0.046 0.147 497 Planarity : 0.005 0.047 601 Dihedral : 5.536 22.410 471 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.18 % Allowed : 25.63 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.51 (0.41), residues: 424 helix: -3.66 (0.71), residues: 24 sheet: -0.08 (0.47), residues: 140 loop : -1.30 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 17 TYR 0.024 0.002 TYR E 351 PHE 0.013 0.002 PHE E 374 TRP 0.028 0.003 TRP H 111 HIS 0.004 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 3392) covalent geometry : angle 0.71456 ( 4614) SS BOND : bond 0.00455 ( 6) SS BOND : angle 0.96937 ( 12) hydrogen bonds : bond 0.03042 ( 93) hydrogen bonds : angle 6.03559 ( 237) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 392 PHE cc_start: 0.9055 (m-80) cc_final: 0.8837 (m-10) REVERT: H 29 PHE cc_start: 0.7899 (t80) cc_final: 0.7305 (t80) REVERT: H 48 MET cc_start: 0.8314 (mmp) cc_final: 0.7706 (mmm) outliers start: 15 outliers final: 13 residues processed: 89 average time/residue: 0.0874 time to fit residues: 9.0901 Evaluate side-chains 89 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 7.9990 chunk 13 optimal weight: 0.1980 chunk 18 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 30.0000 chunk 23 optimal weight: 30.0000 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 16 optimal weight: 30.0000 chunk 10 optimal weight: 0.0980 overall best weight: 4.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.125638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.096133 restraints weight = 9141.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.098966 restraints weight = 5456.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.100783 restraints weight = 3863.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.101918 restraints weight = 3054.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.102779 restraints weight = 2609.620| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3398 Z= 0.135 Angle : 0.717 7.932 4626 Z= 0.362 Chirality : 0.046 0.153 497 Planarity : 0.004 0.046 601 Dihedral : 5.414 22.953 471 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.90 % Allowed : 25.91 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.37 (0.41), residues: 424 helix: -3.60 (0.72), residues: 24 sheet: 0.07 (0.48), residues: 134 loop : -1.21 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 17 TYR 0.022 0.002 TYR E 351 PHE 0.013 0.002 PHE H 64 TRP 0.028 0.002 TRP H 111 HIS 0.004 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3392) covalent geometry : angle 0.71559 ( 4614) SS BOND : bond 0.00385 ( 6) SS BOND : angle 1.01198 ( 12) hydrogen bonds : bond 0.02958 ( 93) hydrogen bonds : angle 5.89972 ( 237) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 392 PHE cc_start: 0.9032 (m-80) cc_final: 0.8805 (m-10) REVERT: H 29 PHE cc_start: 0.7901 (t80) cc_final: 0.7267 (t80) REVERT: H 48 MET cc_start: 0.8264 (mmp) cc_final: 0.7704 (mmm) outliers start: 14 outliers final: 13 residues processed: 86 average time/residue: 0.0810 time to fit residues: 8.2661 Evaluate side-chains 90 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 8.9990 chunk 40 optimal weight: 0.0470 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 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 = 0.4001 r_free = 0.4001 target = 0.127146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.097698 restraints weight = 9114.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.100507 restraints weight = 5490.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.102330 restraints weight = 3901.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.103589 restraints weight = 3072.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.104334 restraints weight = 2612.710| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3398 Z= 0.125 Angle : 0.742 9.500 4626 Z= 0.369 Chirality : 0.046 0.151 497 Planarity : 0.004 0.046 601 Dihedral : 5.256 23.071 471 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.62 % Allowed : 26.74 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.22 (0.41), residues: 424 helix: -3.71 (0.83), residues: 20 sheet: 0.13 (0.51), residues: 125 loop : -1.07 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 346 TYR 0.024 0.002 TYR E 351 PHE 0.013 0.002 PHE E 374 TRP 0.026 0.002 TRP H 111 HIS 0.005 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3392) covalent geometry : angle 0.73875 ( 4614) SS BOND : bond 0.00372 ( 6) SS BOND : angle 1.60521 ( 12) hydrogen bonds : bond 0.02904 ( 93) hydrogen bonds : angle 5.71581 ( 237) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7781 (t80) cc_final: 0.7105 (t80) REVERT: H 47 TRP cc_start: 0.9249 (t60) cc_final: 0.8561 (t60) REVERT: H 48 MET cc_start: 0.8211 (mmp) cc_final: 0.7957 (mmm) outliers start: 13 outliers final: 13 residues processed: 89 average time/residue: 0.0771 time to fit residues: 8.1897 Evaluate side-chains 92 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.0370 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 41 optimal weight: 30.0000 chunk 37 optimal weight: 50.0000 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 30.0000 chunk 28 optimal weight: 0.9980 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 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 = 0.4020 r_free = 0.4020 target = 0.128634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099261 restraints weight = 9205.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.102258 restraints weight = 5408.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.104159 restraints weight = 3778.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.105498 restraints weight = 2960.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.106237 restraints weight = 2488.032| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3398 Z= 0.126 Angle : 0.725 8.573 4626 Z= 0.367 Chirality : 0.047 0.153 497 Planarity : 0.005 0.045 601 Dihedral : 5.271 22.940 471 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.34 % Allowed : 28.41 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.20 (0.41), residues: 424 helix: -3.49 (0.92), residues: 19 sheet: 0.04 (0.50), residues: 125 loop : -1.02 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 17 TYR 0.024 0.002 TYR E 351 PHE 0.033 0.002 PHE E 497 TRP 0.018 0.002 TRP H 111 HIS 0.002 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3392) covalent geometry : angle 0.72238 ( 4614) SS BOND : bond 0.00426 ( 6) SS BOND : angle 1.30737 ( 12) hydrogen bonds : bond 0.03042 ( 93) hydrogen bonds : angle 5.61413 ( 237) =============================================================================== Job complete usr+sys time: 767.33 seconds wall clock time: 13 minutes 50.11 seconds (830.11 seconds total)