Starting phenix.real_space_refine on Tue Mar 3 12:01:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i52_4410/03_2026/6i52_4410.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i52_4410/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6i52_4410/03_2026/6i52_4410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i52_4410/03_2026/6i52_4410.map" model { file = "/net/cci-nas-00/data/ceres_data/6i52_4410/03_2026/6i52_4410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i52_4410/03_2026/6i52_4410.cif" } 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-dev-5986/lib/python3.9/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: 0.75, per 1000 atoms: 0.19 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: 0.20 Conformation dependent library (CDL) restraints added in 122.2 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: 0.46 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: 0.51 Time building geometry restraints manager: 0.28 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=" C THR B 40 " pdb=" N PRO B 41 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.49e+00 bond pdb=" C ALA C 482 " pdb=" N TYR C 483 " ideal model delta sigma weight residual 1.331 1.356 -0.025 2.07e-02 2.33e+03 1.40e+00 bond pdb=" C3' DT D 11 " pdb=" O3' DT D 11 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" N ARG C 460 " pdb=" CA ARG C 460 " ideal model delta sigma weight residual 1.458 1.477 -0.019 1.90e-02 2.77e+03 1.04e+00 bond pdb=" N ALA B 177 " pdb=" CA ALA B 177 " ideal model delta sigma weight residual 1.468 1.457 0.012 1.24e-02 6.50e+03 8.68e-01 ... (remaining 3949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 5238 1.39 - 2.78: 159 2.78 - 4.17: 24 4.17 - 5.56: 6 5.56 - 6.95: 2 Bond angle restraints: 5429 Sorted by residual: angle pdb=" C GLY C 459 " pdb=" N ARG C 460 " pdb=" CA ARG C 460 " ideal model delta sigma weight residual 121.70 128.65 -6.95 1.80e+00 3.09e-01 1.49e+01 angle pdb=" C GLU C 462 " pdb=" N LYS C 463 " pdb=" CA LYS C 463 " ideal model delta sigma weight residual 123.05 117.73 5.32 1.40e+00 5.10e-01 1.45e+01 angle pdb=" C PHE C 466 " pdb=" N PHE C 467 " pdb=" CA PHE C 467 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.55e+00 angle pdb=" C ILE B 85 " pdb=" N PHE B 86 " pdb=" CA PHE B 86 " ideal model delta sigma weight residual 122.67 118.18 4.49 1.73e+00 3.34e-01 6.74e+00 angle pdb=" C ASP C 465 " pdb=" N PHE C 466 " pdb=" CA PHE C 466 " ideal model delta sigma weight residual 121.54 126.29 -4.75 1.91e+00 2.74e-01 6.18e+00 ... (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: 396 0.027 - 0.054: 137 0.054 - 0.081: 40 0.081 - 0.109: 31 0.109 - 0.136: 14 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=" 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 chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.40e-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: 0.150 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.330 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5551 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 : 0.002 0.050 3954 Z= 0.120 Angle : 0.571 6.949 5429 Z= 0.339 Chirality : 0.039 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 covalent geometry : bond 0.00244 ( 3954) covalent geometry : angle 0.57147 ( 5429) hydrogen bonds : bond 0.15029 ( 108) hydrogen bonds : angle 12.38356 ( 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 : 0.140 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: 0.0718 time to fit residues: 11.2279 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 : 0.136 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 overall best weight: 5.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN A 80 ASN B 167 HIS C 516 ASN C 561 ASN C 573 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.097895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.076942 restraints weight = 30695.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.078114 restraints weight = 26396.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.079017 restraints weight = 23535.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.079739 restraints weight = 21506.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.080287 restraints weight = 19980.092| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3954 Z= 0.215 Angle : 0.805 8.980 5429 Z= 0.439 Chirality : 0.048 0.186 618 Planarity : 0.006 0.050 639 Dihedral : 19.559 147.103 657 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.31 % Favored : 91.98 % Rotamer: Outliers : 0.26 % Allowed : 4.92 % Favored : 94.82 % 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: -3.14 (0.33), residues: 424 helix: -1.29 (0.47), residues: 90 sheet: -1.11 (0.52), residues: 85 loop : -2.89 (0.30), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 578 TYR 0.019 0.003 TYR C 610 PHE 0.020 0.003 PHE A 75 TRP 0.038 0.003 TRP B 101 HIS 0.005 0.002 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 3954) covalent geometry : angle 0.80502 ( 5429) hydrogen bonds : bond 0.04303 ( 108) hydrogen bonds : angle 8.20246 ( 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 61 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 135 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8667 (mmtt) REVERT: B 154 ILE cc_start: 0.7364 (pt) cc_final: 0.7062 (pt) REVERT: B 160 PHE cc_start: 0.7068 (p90) cc_final: 0.6837 (p90) REVERT: C 536 LEU cc_start: 0.9144 (mp) cc_final: 0.8780 (mp) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.0619 time to fit residues: 4.7327 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 : 0.128 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 HIS C 492 ASN C 512 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.094357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.075280 restraints weight = 37483.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.076072 restraints weight = 33959.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.076681 restraints weight = 31360.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.077188 restraints weight = 29485.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.077612 restraints weight = 28022.598| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6123 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3954 Z= 0.187 Angle : 0.735 6.832 5429 Z= 0.397 Chirality : 0.045 0.201 618 Planarity : 0.006 0.056 639 Dihedral : 20.011 146.676 657 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.43 % Favored : 89.86 % Rotamer: Outliers : 0.26 % Allowed : 2.59 % 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: -2.79 (0.35), residues: 424 helix: -0.60 (0.51), residues: 90 sheet: -1.07 (0.56), residues: 82 loop : -2.75 (0.31), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 578 TYR 0.015 0.003 TYR C 610 PHE 0.012 0.003 PHE B 128 TRP 0.013 0.002 TRP C 503 HIS 0.005 0.002 HIS C 600 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 3954) covalent geometry : angle 0.73511 ( 5429) hydrogen bonds : bond 0.03931 ( 108) hydrogen bonds : angle 7.53444 ( 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 58 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.5802 (mpp) cc_final: 0.5499 (mmt) REVERT: B 135 LYS cc_start: 0.8707 (mmtt) cc_final: 0.8507 (mmpt) REVERT: C 475 PHE cc_start: 0.8518 (t80) cc_final: 0.8289 (t80) outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.0545 time to fit residues: 4.0993 Evaluate side-chains 38 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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: 10.9990 chunk 18 optimal weight: 30.0000 chunk 36 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 0.0980 chunk 40 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 40.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.091660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.072820 restraints weight = 38498.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.073654 restraints weight = 34791.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.074339 restraints weight = 31929.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.074894 restraints weight = 29822.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.075360 restraints weight = 28153.807| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3954 Z= 0.162 Angle : 0.717 6.705 5429 Z= 0.385 Chirality : 0.045 0.191 618 Planarity : 0.006 0.070 639 Dihedral : 20.065 147.314 657 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.73 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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 (0.35), residues: 424 helix: -0.60 (0.49), residues: 90 sheet: -1.19 (0.55), residues: 82 loop : -2.78 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 591 TYR 0.019 0.002 TYR C 610 PHE 0.018 0.002 PHE B 71 TRP 0.022 0.003 TRP C 533 HIS 0.007 0.002 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3954) covalent geometry : angle 0.71651 ( 5429) hydrogen bonds : bond 0.03939 ( 108) hydrogen bonds : angle 7.12194 ( 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 57 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.132 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0763 time to fit residues: 5.2993 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 : 0.130 ------------------------------------------------------------------------------- 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: 0.5980 chunk 12 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 8 optimal weight: 40.0000 chunk 19 optimal weight: 0.3980 chunk 18 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 overall best weight: 4.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.089539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.071419 restraints weight = 39745.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.072365 restraints weight = 35284.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.073118 restraints weight = 32073.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.073733 restraints weight = 29662.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.074216 restraints weight = 27826.758| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5534 moved from start: 0.7311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3954 Z= 0.173 Angle : 0.728 6.791 5429 Z= 0.393 Chirality : 0.045 0.198 618 Planarity : 0.006 0.057 639 Dihedral : 20.219 147.431 657 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.61 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % 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: -2.95 (0.35), residues: 424 helix: -0.60 (0.49), residues: 90 sheet: -1.37 (0.54), residues: 82 loop : -2.83 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 22 TYR 0.018 0.003 TYR B 151 PHE 0.014 0.002 PHE B 71 TRP 0.016 0.002 TRP A 72 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 3954) covalent geometry : angle 0.72816 ( 5429) hydrogen bonds : bond 0.03864 ( 108) hydrogen bonds : angle 6.88138 ( 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 51 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.080 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0543 time to fit residues: 3.5432 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 : 0.107 ------------------------------------------------------------------------------- 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: 6.9990 chunk 24 optimal weight: 20.0000 chunk 26 optimal weight: 0.0370 chunk 34 optimal weight: 30.0000 chunk 31 optimal weight: 9.9990 chunk 23 optimal weight: 40.0000 chunk 37 optimal weight: 9.9990 chunk 17 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 overall best weight: 5.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3987 r_free = 0.3987 target = 0.087191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.070404 restraints weight = 40184.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.070987 restraints weight = 37190.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.071450 restraints weight = 34892.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.071833 restraints weight = 33150.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.072083 restraints weight = 31763.263| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.8048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3954 Z= 0.195 Angle : 0.764 6.509 5429 Z= 0.415 Chirality : 0.046 0.184 618 Planarity : 0.005 0.048 639 Dihedral : 20.463 147.584 657 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.14 % Favored : 89.15 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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: -3.23 (0.35), residues: 424 helix: -1.04 (0.45), residues: 91 sheet: -1.69 (0.50), residues: 92 loop : -2.89 (0.34), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 591 TYR 0.021 0.003 TYR C 610 PHE 0.014 0.002 PHE B 71 TRP 0.018 0.002 TRP A 72 HIS 0.008 0.002 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 3954) covalent geometry : angle 0.76429 ( 5429) hydrogen bonds : bond 0.04217 ( 108) hydrogen bonds : angle 7.09111 ( 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 52 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: B 135 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8313 (mmmt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0633 time to fit residues: 4.1434 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 : 0.130 ------------------------------------------------------------------------------- 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: 0.9990 chunk 16 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.088285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.071183 restraints weight = 39382.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.071695 restraints weight = 36910.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.072102 restraints weight = 35061.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.072367 restraints weight = 33595.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.072667 restraints weight = 32541.544| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.8223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3954 Z= 0.156 Angle : 0.712 6.950 5429 Z= 0.388 Chirality : 0.045 0.202 618 Planarity : 0.005 0.045 639 Dihedral : 20.464 149.161 657 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.38 % Favored : 88.92 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: -3.08 (0.35), residues: 424 helix: -0.76 (0.47), residues: 91 sheet: -1.72 (0.48), residues: 95 loop : -2.80 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 99 TYR 0.019 0.002 TYR B 151 PHE 0.013 0.002 PHE B 71 TRP 0.015 0.002 TRP A 72 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 3954) covalent geometry : angle 0.71173 ( 5429) hydrogen bonds : bond 0.04051 ( 108) hydrogen bonds : angle 6.69634 ( 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 48 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.3356 (mmm) cc_final: 0.3023 (tpp) REVERT: B 135 LYS cc_start: 0.8476 (mmtt) cc_final: 0.8198 (mmmt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0624 time to fit residues: 3.8821 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 : 0.140 ------------------------------------------------------------------------------- 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: 20.0000 chunk 10 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 17 optimal weight: 0.3980 chunk 34 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 overall best weight: 6.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.084274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.068352 restraints weight = 40458.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.068762 restraints weight = 37513.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.069301 restraints weight = 35433.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.069663 restraints weight = 33678.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.069850 restraints weight = 32289.829| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.9122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3954 Z= 0.211 Angle : 0.823 10.063 5429 Z= 0.439 Chirality : 0.049 0.188 618 Planarity : 0.006 0.043 639 Dihedral : 20.784 147.403 657 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 0.71 % Allowed : 12.03 % Favored : 87.26 % 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: -3.29 (0.35), residues: 424 helix: -1.04 (0.46), residues: 89 sheet: -1.96 (0.47), residues: 94 loop : -2.83 (0.34), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 591 TYR 0.024 0.003 TYR C 610 PHE 0.022 0.003 PHE B 86 TRP 0.018 0.002 TRP A 72 HIS 0.006 0.002 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 3954) covalent geometry : angle 0.82292 ( 5429) hydrogen bonds : bond 0.04537 ( 108) hydrogen bonds : angle 7.05692 ( 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 47 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: C 586 TYR cc_start: 0.8128 (t80) cc_final: 0.7882 (t80) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0630 time to fit residues: 3.7825 Evaluate side-chains 36 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 30.0000 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 25 optimal weight: 20.0000 chunk 28 optimal weight: 0.0370 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 overall best weight: 2.6864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.087930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.070401 restraints weight = 38104.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.071124 restraints weight = 34766.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.071542 restraints weight = 32316.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.072066 restraints weight = 30590.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.072395 restraints weight = 29145.492| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.9047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3954 Z= 0.150 Angle : 0.726 7.537 5429 Z= 0.395 Chirality : 0.047 0.211 618 Planarity : 0.005 0.046 639 Dihedral : 20.783 150.214 657 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.91 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: -3.13 (0.36), residues: 424 helix: -0.80 (0.48), residues: 91 sheet: -1.91 (0.46), residues: 100 loop : -2.77 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 60 TYR 0.018 0.002 TYR B 151 PHE 0.032 0.002 PHE C 475 TRP 0.011 0.001 TRP A 72 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 3954) covalent geometry : angle 0.72631 ( 5429) hydrogen bonds : bond 0.04196 ( 108) hydrogen bonds : angle 6.66528 ( 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 51 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 135 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8209 (mmmt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0603 time to fit residues: 3.9413 Evaluate side-chains 36 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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: 8.9990 chunk 15 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 31 optimal weight: 30.0000 chunk 4 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 40.0000 chunk 5 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 0.0040 overall best weight: 2.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3993 r_free = 0.3993 target = 0.088814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.071278 restraints weight = 39193.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.072049 restraints weight = 35330.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.072652 restraints weight = 32584.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.072960 restraints weight = 30556.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.073447 restraints weight = 29393.514| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.9220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3954 Z= 0.149 Angle : 0.730 9.214 5429 Z= 0.393 Chirality : 0.046 0.207 618 Planarity : 0.005 0.042 639 Dihedral : 20.748 150.435 657 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.91 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -3.06 (0.36), residues: 424 helix: -0.69 (0.48), residues: 91 sheet: -1.90 (0.45), residues: 103 loop : -2.72 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 591 TYR 0.019 0.002 TYR B 151 PHE 0.014 0.002 PHE C 467 TRP 0.008 0.001 TRP C 503 HIS 0.003 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 3954) covalent geometry : angle 0.72972 ( 5429) hydrogen bonds : bond 0.03936 ( 108) hydrogen bonds : angle 6.53230 ( 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 48 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.2508 (mmm) cc_final: 0.2303 (tpp) REVERT: B 135 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8095 (mmmt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0584 time to fit residues: 3.6222 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 : 0.087 ------------------------------------------------------------------------------- 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: 7.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 0.0030 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 30.0000 chunk 36 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 overall best weight: 5.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3948 r_free = 0.3948 target = 0.085425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.068782 restraints weight = 40254.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.069410 restraints weight = 36959.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.069867 restraints weight = 34651.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.070242 restraints weight = 32855.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.070578 restraints weight = 31472.143| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.9863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3954 Z= 0.183 Angle : 0.779 7.129 5429 Z= 0.420 Chirality : 0.048 0.184 618 Planarity : 0.005 0.045 639 Dihedral : 21.000 150.042 657 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.71 % Allowed : 12.26 % Favored : 87.03 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -3.11 (0.36), residues: 424 helix: -0.68 (0.49), residues: 91 sheet: -2.07 (0.47), residues: 98 loop : -2.71 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 578 TYR 0.022 0.003 TYR C 610 PHE 0.018 0.003 PHE C 475 TRP 0.014 0.002 TRP A 72 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 3954) covalent geometry : angle 0.77860 ( 5429) hydrogen bonds : bond 0.04267 ( 108) hydrogen bonds : angle 6.82959 ( 294) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 840.61 seconds wall clock time: 15 minutes 10.21 seconds (910.21 seconds total)