Starting phenix.real_space_refine on Thu Sep 10 21:21:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i52_4410/09_2026/6i52_4410.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i52_4410/09_2026/6i52_4410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6i52_4410/09_2026/6i52_4410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i52_4410/09_2026/6i52_4410.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6i52_4410/09_2026/6i52_4410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i52_4410/09_2026/6i52_4410.map" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 16 5.16 5 C 2377 2.51 5 N 635 2.21 5 O 808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3856 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 966 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1041 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 1 Chain: "C" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1449 Classifications: {'peptide': 178} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 171} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 400 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Time building chain proxies: 1.01, per 1000 atoms: 0.26 Number of scatterers: 3856 At special positions: 0 Unit cell: (82.68, 65.72, 107.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 20 15.00 O 808 8.00 N 635 7.00 C 2377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 80.8 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: 828 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 22.9% alpha, 24.1% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 9 through 15 removed outlier: 3.969A pdb=" N ILE A 13 " --> pdb=" O PRO A 10 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 14 " --> pdb=" O THR A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.682A pdb=" N LYS A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 50 Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.704A pdb=" N LEU B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 455 removed outlier: 3.590A pdb=" N GLN C 454 " --> pdb=" O ILE C 450 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 450 through 455' Processing helix chain 'C' and resid 537 through 546 removed outlier: 3.646A pdb=" N LEU C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 557 Processing helix chain 'C' and resid 561 through 571 Processing helix chain 'C' and resid 604 through 617 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 6.827A pdb=" N ARG A 78 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE A 89 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.877A pdb=" N ILE A 37 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.712A pdb=" N SER B 61 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.131A pdb=" N GLY B 73 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL B 134 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 80 Processing sheet with id=AA6, first strand: chain 'C' and resid 468 through 476 removed outlier: 4.815A pdb=" N ILE C 473 " --> pdb=" O ILE C 526 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE C 526 " --> pdb=" O ILE C 473 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N GLN C 531 " --> pdb=" O ILE C 592 " (cutoff:3.500A) removed outlier: 10.480A pdb=" N TYR C 594 " --> pdb=" O GLN C 531 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP C 533 " --> pdb=" O TYR C 594 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL C 596 " --> pdb=" O TRP C 533 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR C 535 " --> pdb=" O VAL C 596 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASN C 598 " --> pdb=" O THR C 535 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG C 591 " --> pdb=" O ASP C 584 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP C 584 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG C 580 " --> pdb=" O THR C 595 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG C 578 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU C 599 " --> pdb=" O ASP C 576 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP C 576 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 482 through 484 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 497 108 hydrogen bonds defined for protein. 294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 0.55 Time building geometry restraints manager: 0.37 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: 1129 1.34 - 1.45: 627 1.45 - 1.57: 2136 1.57 - 1.69: 39 1.69 - 1.81: 23 Bond restraints: 3954 Sorted by residual: bond pdb=" C3' DT D 11 " pdb=" C2' DT D 11 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.14e+00 bond pdb=" C3' DT D 13 " pdb=" C2' DT D 13 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.26e+00 bond pdb=" C1' DT D 13 " pdb=" N1 DT D 13 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.81e+00 bond pdb=" C1' DT D 21 " pdb=" N1 DT D 21 " ideal model delta sigma weight residual 1.468 1.499 -0.031 1.40e-02 5.10e+03 4.93e+00 bond pdb=" C1' DT D 18 " pdb=" N1 DT D 18 " ideal model delta sigma weight residual 1.468 1.498 -0.030 1.40e-02 5.10e+03 4.51e+00 ... (remaining 3949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 5155 1.39 - 2.78: 238 2.78 - 4.17: 28 4.17 - 5.56: 6 5.56 - 6.95: 2 Bond angle restraints: 5429 Sorted by residual: angle pdb=" N3 DT D 12 " pdb=" C4 DT D 12 " pdb=" O4 DT D 12 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT D 26 " pdb=" C4 DT D 26 " pdb=" O4 DT D 26 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT D 23 " pdb=" C4 DT D 23 " pdb=" O4 DT D 23 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT D 8 " pdb=" C4 DT D 8 " pdb=" O4 DT D 8 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT D 27 " pdb=" C4 DT D 27 " pdb=" O4 DT D 27 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 5424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.30: 2228 29.30 - 58.61: 90 58.61 - 87.91: 15 87.91 - 117.21: 2 117.21 - 146.51: 3 Dihedral angle restraints: 2338 sinusoidal: 1070 harmonic: 1268 Sorted by residual: dihedral pdb=" CA GLU C 462 " pdb=" C GLU C 462 " pdb=" N LYS C 463 " pdb=" CA LYS C 463 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA PHE C 466 " pdb=" C PHE C 466 " pdb=" N PHE C 467 " pdb=" CA PHE C 467 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C4' DT D 11 " pdb=" C3' DT D 11 " pdb=" O3' DT D 11 " pdb=" P DT D 12 " ideal model delta sinusoidal sigma weight residual 220.00 73.49 146.51 1 3.50e+01 8.16e-04 1.44e+01 ... (remaining 2335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 359 0.027 - 0.054: 154 0.054 - 0.081: 51 0.081 - 0.109: 38 0.109 - 0.136: 16 Chirality restraints: 618 Sorted by residual: chirality pdb=" CA THR B 79 " pdb=" N THR B 79 " pdb=" C THR B 79 " pdb=" CB THR B 79 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" C3' DT D 11 " pdb=" C4' DT D 11 " pdb=" O3' DT D 11 " pdb=" C2' DT D 11 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE A 24 " pdb=" N ILE A 24 " pdb=" C ILE A 24 " pdb=" CB ILE A 24 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.60e-01 ... (remaining 615 not shown) Planarity restraints: 639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 79 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C THR B 79 " 0.043 2.00e-02 2.50e+03 pdb=" O THR B 79 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP B 80 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 30 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 31 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 118 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO A 119 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " 0.019 5.00e-02 4.00e+02 ... (remaining 636 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1101 2.82 - 3.34: 3351 3.34 - 3.86: 6120 3.86 - 4.38: 6724 4.38 - 4.90: 11453 Nonbonded interactions: 28749 Sorted by model distance: nonbonded pdb=" OD2 ASP A 9 " pdb=" OG1 THR A 11 " model vdw 2.303 3.040 nonbonded pdb=" ND1 HIS B 68 " pdb=" O GLY B 138 " model vdw 2.326 3.120 nonbonded pdb=" OD1 ASP C 500 " pdb=" N GLY C 501 " model vdw 2.330 3.120 nonbonded pdb=" OG SER C 474 " pdb=" O SER C 524 " model vdw 2.339 3.040 nonbonded pdb=" O VAL B 163 " pdb=" ND1 HIS B 166 " model vdw 2.361 3.120 ... (remaining 28744 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.830 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5414 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 0.050 3954 Z= 0.262 Angle : 0.642 6.949 5429 Z= 0.515 Chirality : 0.042 0.136 618 Planarity : 0.004 0.047 639 Dihedral : 16.564 146.514 1510 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.94 % Allowed : 11.56 % Favored : 87.50 % Rotamer: Outliers : 5.70 % Allowed : 9.84 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % 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: -4.07 (0.31), residues: 424 helix: -3.47 (0.33), residues: 95 sheet: -1.85 (0.49), residues: 77 loop : -2.75 (0.30), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 591 TYR 0.010 0.001 TYR B 151 PHE 0.016 0.001 PHE C 467 TRP 0.004 0.001 TRP C 533 HIS 0.002 0.000 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.26 ( 3954) covalent geometry : angle 0.64241 / 0.52 ( 5429) hydrogen bonds : bond 0.15029 / 10.30 ( 108) hydrogen bonds : angle 12.38356 / 8.43 ( 294) *********************** 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 134 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.6037 (OUTLIER) cc_final: 0.5038 (mp10) REVERT: A 53 MET cc_start: 0.6572 (mtm) cc_final: 0.6343 (mpp) REVERT: A 75 PHE cc_start: 0.7684 (t80) cc_final: 0.7453 (t80) REVERT: B 160 PHE cc_start: 0.6461 (p90) cc_final: 0.6220 (p90) REVERT: B 167 HIS cc_start: 0.8149 (m-70) cc_final: 0.7539 (t-170) REVERT: C 478 VAL cc_start: 0.4301 (OUTLIER) cc_final: 0.3902 (t) REVERT: C 479 ASP cc_start: 0.8308 (m-30) cc_final: 0.7717 (p0) REVERT: C 531 GLN cc_start: 0.7691 (pt0) cc_final: 0.7128 (tm-30) outliers start: 22 outliers final: 6 residues processed: 129 average time/residue: 0.0692 time to fit residues: 10.8509 Evaluate side-chains 54 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 0.0570 chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 overall best weight: 3.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN A 35 GLN A 80 ASN B 63 ASN ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.104013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.082935 restraints weight = 31245.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.084206 restraints weight = 26764.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.085212 restraints weight = 23761.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.086043 restraints weight = 21583.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.086605 restraints weight = 19878.491| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5793 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3954 Z= 0.169 Angle : 0.739 8.354 5429 Z= 0.403 Chirality : 0.049 0.250 618 Planarity : 0.007 0.083 639 Dihedral : 19.539 146.240 657 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.31 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % 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: -3.04 (0.34), residues: 424 helix: -1.34 (0.49), residues: 89 sheet: -1.10 (0.55), residues: 77 loop : -2.71 (0.31), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 578 TYR 0.022 0.002 TYR B 151 PHE 0.021 0.003 PHE A 75 TRP 0.039 0.003 TRP B 101 HIS 0.007 0.002 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 ( 3954) covalent geometry : angle 0.73943 / 0.40 ( 5429) hydrogen bonds : bond 0.03874 / 2.75 ( 108) hydrogen bonds : angle 8.66127 / 5.86 ( 294) *********************** 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 69 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: A 75 PHE cc_start: 0.7549 (t80) cc_final: 0.6272 (t80) REVERT: B 135 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8556 (mmtt) REVERT: B 160 PHE cc_start: 0.7112 (p90) cc_final: 0.6903 (p90) REVERT: C 532 LEU cc_start: 0.6761 (tp) cc_final: 0.6538 (mm) REVERT: C 536 LEU cc_start: 0.9167 (mp) cc_final: 0.8837 (mp) REVERT: C 584 ASP cc_start: 0.8705 (m-30) cc_final: 0.8306 (p0) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0650 time to fit residues: 5.5679 Evaluate side-chains 40 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 43 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 ASN C 516 ASN C 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.097129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.077585 restraints weight = 36259.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.078370 restraints weight = 33127.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.078993 restraints weight = 30902.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.079508 restraints weight = 29193.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.079895 restraints weight = 27841.920| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3954 Z= 0.167 Angle : 0.692 7.689 5429 Z= 0.380 Chirality : 0.048 0.277 618 Planarity : 0.006 0.057 639 Dihedral : 19.586 147.050 657 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.49 % Favored : 90.80 % Rotamer: Outliers : 0.26 % Allowed : 3.89 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.35), residues: 424 helix: -0.85 (0.50), residues: 90 sheet: -0.97 (0.53), residues: 90 loop : -2.81 (0.31), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 22 TYR 0.018 0.002 TYR C 610 PHE 0.026 0.003 PHE B 71 TRP 0.012 0.002 TRP A 72 HIS 0.010 0.002 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 ( 3954) covalent geometry : angle 0.69180 / 0.38 ( 5429) hydrogen bonds : bond 0.03957 / 2.77 ( 108) hydrogen bonds : angle 7.66200 / 5.24 ( 294) *********************** 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 63 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5907 (mpp) cc_final: 0.5560 (mmt) REVERT: B 135 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8467 (pptt) REVERT: B 137 PHE cc_start: 0.8735 (m-80) cc_final: 0.8501 (m-80) REVERT: B 154 ILE cc_start: 0.7003 (pt) cc_final: 0.6555 (pt) REVERT: B 180 MET cc_start: 0.5778 (tpt) cc_final: 0.5545 (tpt) REVERT: C 536 LEU cc_start: 0.9321 (mp) cc_final: 0.9027 (mp) REVERT: C 572 MET cc_start: 0.8083 (ptt) cc_final: 0.7367 (ppp) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.0657 time to fit residues: 5.2263 Evaluate side-chains 39 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 50.0000 chunk 18 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 14 optimal weight: 0.0020 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 40 optimal weight: 0.0980 chunk 31 optimal weight: 0.0370 chunk 10 optimal weight: 2.9990 overall best weight: 1.4270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN C 531 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.097610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.078270 restraints weight = 37000.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.079061 restraints weight = 33943.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.079704 restraints weight = 31553.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.080213 restraints weight = 29694.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.080559 restraints weight = 28240.576| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3954 Z= 0.136 Angle : 0.671 6.628 5429 Z= 0.364 Chirality : 0.047 0.289 618 Planarity : 0.005 0.060 639 Dihedral : 19.643 146.792 657 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.31 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.36), residues: 424 helix: -0.78 (0.50), residues: 89 sheet: -0.84 (0.56), residues: 82 loop : -2.51 (0.33), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 578 TYR 0.023 0.002 TYR B 151 PHE 0.009 0.002 PHE B 160 TRP 0.013 0.002 TRP C 533 HIS 0.005 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 ( 3954) covalent geometry : angle 0.67114 / 0.36 ( 5429) hydrogen bonds : bond 0.03493 / 2.46 ( 108) hydrogen bonds : angle 7.39388 / 4.98 ( 294) *********************** 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 61 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.084 Fit side-chains REVERT: A 53 MET cc_start: 0.5853 (mpp) cc_final: 0.5432 (mmt) REVERT: B 135 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8536 (pptt) REVERT: B 137 PHE cc_start: 0.8583 (m-80) cc_final: 0.8272 (m-80) REVERT: B 160 PHE cc_start: 0.6904 (p90) cc_final: 0.6503 (p90) REVERT: B 180 MET cc_start: 0.5575 (tpt) cc_final: 0.5361 (tpt) REVERT: C 532 LEU cc_start: 0.6817 (tp) cc_final: 0.6126 (mm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0650 time to fit residues: 5.0102 Evaluate side-chains 38 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.0980 chunk 12 optimal weight: 0.2980 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 20 optimal weight: 40.0000 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 40.0000 chunk 36 optimal weight: 4.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN ** C 540 GLN ** 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 = 0.4156 r_free = 0.4156 target = 0.097248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.080011 restraints weight = 38092.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.080672 restraints weight = 35123.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.081225 restraints weight = 32891.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.081676 restraints weight = 31133.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.082066 restraints weight = 29701.158| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3954 Z= 0.142 Angle : 0.663 7.159 5429 Z= 0.362 Chirality : 0.046 0.287 618 Planarity : 0.006 0.073 639 Dihedral : 19.676 146.547 657 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.49 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.35), residues: 424 helix: -0.88 (0.47), residues: 92 sheet: -0.94 (0.57), residues: 82 loop : -2.55 (0.32), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 113 TYR 0.019 0.002 TYR B 151 PHE 0.009 0.002 PHE A 75 TRP 0.015 0.002 TRP A 72 HIS 0.010 0.002 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 3954) covalent geometry : angle 0.66327 / 0.36 ( 5429) hydrogen bonds : bond 0.03586 / 2.37 ( 108) hydrogen bonds : angle 7.14707 / 4.86 ( 294) *********************** 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 56 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5780 (mpp) cc_final: 0.5479 (mmt) REVERT: A 75 PHE cc_start: 0.7453 (t80) cc_final: 0.7160 (t80) REVERT: B 180 MET cc_start: 0.5821 (tpt) cc_final: 0.5596 (tpt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0675 time to fit residues: 4.9028 Evaluate side-chains 35 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 0.0030 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 512 ASN ** C 540 GLN ** 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 = 0.4125 r_free = 0.4125 target = 0.095782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.076872 restraints weight = 38127.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.077688 restraints weight = 34768.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.078376 restraints weight = 32191.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.078950 restraints weight = 30172.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.079422 restraints weight = 28553.845| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3954 Z= 0.139 Angle : 0.653 7.588 5429 Z= 0.357 Chirality : 0.047 0.288 618 Planarity : 0.005 0.052 639 Dihedral : 19.741 146.561 657 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.96 % Favored : 90.33 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.36), residues: 424 helix: -0.81 (0.47), residues: 92 sheet: -0.91 (0.57), residues: 82 loop : -2.51 (0.33), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 22 TYR 0.021 0.002 TYR B 151 PHE 0.010 0.002 PHE A 75 TRP 0.015 0.002 TRP A 72 HIS 0.005 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 3954) covalent geometry : angle 0.65262 / 0.36 ( 5429) hydrogen bonds : bond 0.03520 / 2.47 ( 108) hydrogen bonds : angle 6.87959 / 4.72 ( 294) *********************** 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 54 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.108 Fit side-chains REVERT: A 53 MET cc_start: 0.5646 (mpp) cc_final: 0.5430 (mmt) REVERT: A 63 MET cc_start: 0.6446 (mmp) cc_final: 0.5986 (mmt) REVERT: B 135 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8440 (mmmt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0573 time to fit residues: 4.0129 Evaluate side-chains 34 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 40.0000 chunk 35 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** 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 = 0.4049 r_free = 0.4049 target = 0.090434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.071982 restraints weight = 39437.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.072536 restraints weight = 36267.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.073176 restraints weight = 34075.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.073640 restraints weight = 32216.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.073934 restraints weight = 30759.289| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 moved from start: 0.7182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3954 Z= 0.199 Angle : 0.781 9.267 5429 Z= 0.421 Chirality : 0.050 0.294 618 Planarity : 0.006 0.073 639 Dihedral : 20.046 145.502 657 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.85 % Favored : 88.44 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.36), residues: 424 helix: -0.70 (0.49), residues: 90 sheet: -1.30 (0.56), residues: 82 loop : -2.68 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 7 TYR 0.019 0.003 TYR C 610 PHE 0.017 0.003 PHE A 87 TRP 0.015 0.002 TRP A 72 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 ( 3954) covalent geometry : angle 0.78106 / 0.42 ( 5429) hydrogen bonds : bond 0.04022 / 2.66 ( 108) hydrogen bonds : angle 7.12090 / 4.90 ( 294) *********************** 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 51 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.138 Fit side-chains REVERT: A 53 MET cc_start: 0.5874 (mpp) cc_final: 0.5296 (mmm) REVERT: A 63 MET cc_start: 0.6202 (mmp) cc_final: 0.5898 (mmt) REVERT: B 135 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8197 (mmmt) REVERT: B 160 PHE cc_start: 0.6952 (p90) cc_final: 0.6519 (p90) REVERT: C 536 LEU cc_start: 0.9251 (mp) cc_final: 0.9011 (mp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0559 time to fit residues: 3.6707 Evaluate side-chains 34 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 32 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 42 optimal weight: 50.0000 chunk 14 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 GLN ** 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 = 0.4049 r_free = 0.4049 target = 0.090804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.072099 restraints weight = 38941.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.072867 restraints weight = 35727.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.073454 restraints weight = 33331.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.073915 restraints weight = 31467.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.074286 restraints weight = 30013.692| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5421 moved from start: 0.7480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3954 Z= 0.162 Angle : 0.734 7.676 5429 Z= 0.393 Chirality : 0.049 0.283 618 Planarity : 0.005 0.049 639 Dihedral : 20.183 147.317 657 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.38 % Favored : 88.92 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.37), residues: 424 helix: -0.75 (0.49), residues: 90 sheet: -1.27 (0.57), residues: 82 loop : -2.58 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 7 TYR 0.021 0.003 TYR C 586 PHE 0.010 0.002 PHE A 75 TRP 0.017 0.002 TRP A 72 HIS 0.006 0.001 HIS C 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 3954) covalent geometry : angle 0.73409 / 0.39 ( 5429) hydrogen bonds : bond 0.03713 / 2.55 ( 108) hydrogen bonds : angle 6.93081 / 4.79 ( 294) *********************** 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 51 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.137 Fit side-chains REVERT: B 135 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8435 (ptmm) REVERT: B 160 PHE cc_start: 0.7034 (p90) cc_final: 0.6680 (p90) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0564 time to fit residues: 3.7444 Evaluate side-chains 33 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 33 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 63 ASN ** B 95 GLN ** 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 = 0.4046 r_free = 0.4046 target = 0.090319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.073520 restraints weight = 40069.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.074083 restraints weight = 37383.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.074547 restraints weight = 35302.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.074922 restraints weight = 33664.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.075195 restraints weight = 32401.760| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.7631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3954 Z= 0.147 Angle : 0.719 7.935 5429 Z= 0.385 Chirality : 0.050 0.303 618 Planarity : 0.005 0.047 639 Dihedral : 20.180 147.593 657 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.14 % Favored : 89.15 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.36), residues: 424 helix: -0.79 (0.48), residues: 92 sheet: -1.32 (0.56), residues: 82 loop : -2.71 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 7 TYR 0.021 0.002 TYR B 151 PHE 0.009 0.002 PHE A 75 TRP 0.013 0.002 TRP C 533 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 ( 3954) covalent geometry : angle 0.71941 / 0.39 ( 5429) hydrogen bonds : bond 0.03712 / 2.55 ( 108) hydrogen bonds : angle 6.70298 / 4.61 ( 294) *********************** 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 47 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: B 135 LYS cc_start: 0.8557 (mmtt) cc_final: 0.8290 (ptmm) REVERT: C 536 LEU cc_start: 0.9269 (mp) cc_final: 0.9009 (mp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0525 time to fit residues: 3.2719 Evaluate side-chains 35 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 23 optimal weight: 9.9990 chunk 15 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 GLN ** 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 = 0.3999 r_free = 0.3999 target = 0.086711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.070312 restraints weight = 39306.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.070996 restraints weight = 35573.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.071527 restraints weight = 32870.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.071939 restraints weight = 30903.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.072264 restraints weight = 29412.321| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.8372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3954 Z= 0.205 Angle : 0.803 7.356 5429 Z= 0.434 Chirality : 0.053 0.289 618 Planarity : 0.006 0.050 639 Dihedral : 20.349 146.454 657 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.71 % Allowed : 11.79 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % 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: -3.19 (0.35), residues: 424 helix: -1.07 (0.46), residues: 90 sheet: -1.63 (0.54), residues: 82 loop : -2.82 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 60 TYR 0.021 0.003 TYR B 151 PHE 0.013 0.002 PHE B 143 TRP 0.018 0.003 TRP C 533 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 ( 3954) covalent geometry : angle 0.80312 / 0.43 ( 5429) hydrogen bonds : bond 0.04438 / 2.99 ( 108) hydrogen bonds : angle 7.18359 / 4.93 ( 294) ********************** 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 49 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.146 Fit side-chains REVERT: A 63 MET cc_start: 0.6181 (mmp) cc_final: 0.5856 (mmt) REVERT: B 135 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8337 (mmmt) REVERT: C 531 GLN cc_start: 0.8043 (pt0) cc_final: 0.7837 (tm-30) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0653 time to fit residues: 4.1465 Evaluate side-chains 37 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 5 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 15 optimal weight: 0.0030 chunk 36 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 40.0000 chunk 26 optimal weight: 7.9990 overall best weight: 4.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 GLN ** 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 = 0.4013 r_free = 0.4013 target = 0.087687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.070888 restraints weight = 39656.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.071302 restraints weight = 37755.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.071618 restraints weight = 36305.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.071874 restraints weight = 35110.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 13)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.072035 restraints weight = 34130.463| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.8557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3954 Z= 0.163 Angle : 0.730 7.128 5429 Z= 0.394 Chirality : 0.050 0.279 618 Planarity : 0.005 0.045 639 Dihedral : 20.503 148.418 657 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.38 % Favored : 88.92 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % 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: -3.24 (0.36), residues: 424 helix: -1.08 (0.46), residues: 92 sheet: -1.77 (0.51), residues: 92 loop : -2.85 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 578 TYR 0.018 0.002 TYR C 586 PHE 0.011 0.002 PHE A 75 TRP 0.017 0.002 TRP C 533 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 ( 3954) covalent geometry : angle 0.72990 / 0.39 ( 5429) hydrogen bonds : bond 0.03986 / 2.72 ( 108) hydrogen bonds : angle 7.05236 / 4.81 ( 294) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 876.81 seconds wall clock time: 15 minutes 53.81 seconds (953.81 seconds total)