Starting phenix.real_space_refine on Wed Mar 4 02:55:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pdp_71539/03_2026/9pdp_71539.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pdp_71539/03_2026/9pdp_71539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pdp_71539/03_2026/9pdp_71539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pdp_71539/03_2026/9pdp_71539.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pdp_71539/03_2026/9pdp_71539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pdp_71539/03_2026/9pdp_71539.map" } resolution = 3.83 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= 0.022 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 6180 2.51 5 N 1860 2.21 5 O 2064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10140 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 845 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain: "B" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 845 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain: "C" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 845 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain: "D" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 845 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain: "E" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 845 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain: "F" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 845 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain: "G" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 845 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain: "H" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 845 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain: "I" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 845 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain: "J" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 845 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain: "K" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 845 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain: "L" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 845 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 106} Time building chain proxies: 2.55, per 1000 atoms: 0.25 Number of scatterers: 10140 At special positions: 0 Unit cell: (74.76, 69.42, 163.404, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 2064 8.00 N 1860 7.00 C 6180 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: 0.68 Conformation dependent library (CDL) restraints added in 551.0 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 98.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 605 through 710 removed outlier: 3.570A pdb=" N VAL A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 648 " --> pdb=" O GLN A 644 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 710 removed outlier: 4.432A pdb=" N ALA B 648 " --> pdb=" O GLN B 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 710 removed outlier: 4.095A pdb=" N ALA C 648 " --> pdb=" O GLN C 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 710 removed outlier: 4.625A pdb=" N ALA D 648 " --> pdb=" O GLN D 644 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 710 removed outlier: 3.574A pdb=" N VAL E 609 " --> pdb=" O ASP E 605 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA E 648 " --> pdb=" O GLN E 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 710 removed outlier: 3.512A pdb=" N VAL F 609 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA F 648 " --> pdb=" O GLN F 644 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER F 710 " --> pdb=" O ASN F 706 " (cutoff:3.500A) Processing helix chain 'G' and resid 605 through 710 removed outlier: 4.769A pdb=" N ALA G 648 " --> pdb=" O GLN G 644 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ARG G 649 " --> pdb=" O LEU G 645 " (cutoff:3.500A) Processing helix chain 'H' and resid 605 through 710 removed outlier: 4.285A pdb=" N ALA H 648 " --> pdb=" O GLN H 644 " (cutoff:3.500A) Processing helix chain 'I' and resid 605 through 710 removed outlier: 4.588A pdb=" N ALA I 648 " --> pdb=" O GLN I 644 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG I 649 " --> pdb=" O LEU I 645 " (cutoff:3.500A) Processing helix chain 'J' and resid 605 through 710 removed outlier: 4.320A pdb=" N ALA J 648 " --> pdb=" O GLN J 644 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER J 710 " --> pdb=" O ASN J 706 " (cutoff:3.500A) Processing helix chain 'K' and resid 605 through 645 Processing helix chain 'K' and resid 646 through 710 Processing helix chain 'L' and resid 605 through 710 removed outlier: 3.561A pdb=" N VAL L 609 " --> pdb=" O ASP L 605 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA L 648 " --> pdb=" O GLN L 644 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG L 649 " --> pdb=" O LEU L 645 " (cutoff:3.500A) 1198 hydrogen bonds defined for protein. 3594 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 0.91 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: 3730 1.34 - 1.46: 905 1.46 - 1.57: 5493 1.57 - 1.69: 0 1.69 - 1.80: 72 Bond restraints: 10200 Sorted by residual: bond pdb=" CA GLN K 644 " pdb=" C GLN K 644 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.80e-02 3.09e+03 1.46e+01 bond pdb=" CA GLN A 644 " pdb=" C GLN A 644 " ideal model delta sigma weight residual 1.522 1.492 0.029 1.72e-02 3.38e+03 2.93e+00 bond pdb=" CA GLN I 644 " pdb=" C GLN I 644 " ideal model delta sigma weight residual 1.518 1.461 0.057 4.01e-02 6.22e+02 2.02e+00 bond pdb=" CG LEU I 659 " pdb=" CD1 LEU I 659 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.73e+00 bond pdb=" C ASN A 643 " pdb=" N GLN A 644 " ideal model delta sigma weight residual 1.333 1.314 0.019 1.56e-02 4.11e+03 1.47e+00 ... (remaining 10195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 13453 2.11 - 4.22: 220 4.22 - 6.33: 26 6.33 - 8.44: 3 8.44 - 10.55: 2 Bond angle restraints: 13704 Sorted by residual: angle pdb=" N LEU C 645 " pdb=" CA LEU C 645 " pdb=" C LEU C 645 " ideal model delta sigma weight residual 113.88 108.21 5.67 1.23e+00 6.61e-01 2.12e+01 angle pdb=" N LEU H 645 " pdb=" CA LEU H 645 " pdb=" C LEU H 645 " ideal model delta sigma weight residual 114.04 108.90 5.14 1.24e+00 6.50e-01 1.72e+01 angle pdb=" N LEU I 645 " pdb=" CA LEU I 645 " pdb=" C LEU I 645 " ideal model delta sigma weight residual 114.56 109.48 5.08 1.27e+00 6.20e-01 1.60e+01 angle pdb=" N LEU J 645 " pdb=" CA LEU J 645 " pdb=" C LEU J 645 " ideal model delta sigma weight residual 113.88 109.32 4.56 1.23e+00 6.61e-01 1.38e+01 angle pdb=" N LEU L 645 " pdb=" CA LEU L 645 " pdb=" C LEU L 645 " ideal model delta sigma weight residual 114.31 109.61 4.70 1.29e+00 6.01e-01 1.33e+01 ... (remaining 13699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5564 17.91 - 35.83: 674 35.83 - 53.74: 124 53.74 - 71.66: 70 71.66 - 89.57: 36 Dihedral angle restraints: 6468 sinusoidal: 2664 harmonic: 3804 Sorted by residual: dihedral pdb=" CA LEU D 645 " pdb=" C LEU D 645 " pdb=" N ASN D 646 " pdb=" CA ASN D 646 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LEU I 645 " pdb=" C LEU I 645 " pdb=" N ASN I 646 " pdb=" CA ASN I 646 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA LEU G 645 " pdb=" C LEU G 645 " pdb=" N ASN G 646 " pdb=" CA ASN G 646 " ideal model delta harmonic sigma weight residual 180.00 158.67 21.33 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 6465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1330 0.053 - 0.106: 184 0.106 - 0.160: 27 0.160 - 0.213: 6 0.213 - 0.266: 1 Chirality restraints: 1548 Sorted by residual: chirality pdb=" CG LEU K 645 " pdb=" CB LEU K 645 " pdb=" CD1 LEU K 645 " pdb=" CD2 LEU K 645 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CG LEU I 645 " pdb=" CB LEU I 645 " pdb=" CD1 LEU I 645 " pdb=" CD2 LEU I 645 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CG LEU D 645 " pdb=" CB LEU D 645 " pdb=" CD1 LEU D 645 " pdb=" CD2 LEU D 645 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 1545 not shown) Planarity restraints: 1896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP L 605 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO L 606 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO L 606 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 606 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 605 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO E 606 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 606 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 606 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 605 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO H 606 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO H 606 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 606 " -0.027 5.00e-02 4.00e+02 ... (remaining 1893 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 153 2.68 - 3.24: 11159 3.24 - 3.79: 17844 3.79 - 4.35: 20075 4.35 - 4.90: 33825 Nonbonded interactions: 83056 Sorted by model distance: nonbonded pdb=" OE1 GLU C 667 " pdb=" NH1 ARG D 666 " model vdw 2.129 3.120 nonbonded pdb=" OE1 GLU D 664 " pdb=" NH2 ARG E 666 " model vdw 2.266 3.120 nonbonded pdb=" NE2 GLN A 662 " pdb=" OE2 GLU L 664 " model vdw 2.306 3.120 nonbonded pdb=" O LEU K 645 " pdb=" NH2 ARG K 649 " model vdw 2.319 3.120 nonbonded pdb=" O LEU D 645 " pdb=" NH2 ARG D 649 " model vdw 2.351 3.120 ... (remaining 83051 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.00 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: 8.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.380 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.005 0.069 10200 Z= 0.285 Angle : 0.702 10.554 13704 Z= 0.421 Chirality : 0.040 0.266 1548 Planarity : 0.005 0.055 1896 Dihedral : 18.488 89.570 3948 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.19), residues: 1272 helix: 0.19 (0.13), residues: 1056 sheet: None (None), residues: 0 loop : 0.78 (0.34), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 684 PHE 0.020 0.002 PHE A 675 HIS 0.011 0.004 HIS K 698 Details of bonding type rmsd covalent geometry : bond 0.00531 (10200) covalent geometry : angle 0.70155 (13704) hydrogen bonds : bond 0.09637 ( 1198) hydrogen bonds : angle 4.40958 ( 3594) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 407 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 655 ASN cc_start: 0.8858 (t0) cc_final: 0.8597 (t0) REVERT: A 662 GLN cc_start: 0.5892 (pt0) cc_final: 0.5488 (pt0) REVERT: D 674 SER cc_start: 0.8669 (m) cc_final: 0.8413 (t) REVERT: D 681 GLU cc_start: 0.7737 (tp30) cc_final: 0.7378 (tp30) REVERT: E 669 LEU cc_start: 0.9354 (mt) cc_final: 0.8862 (tt) REVERT: H 635 ASP cc_start: 0.8330 (t70) cc_final: 0.8010 (t70) REVERT: H 674 SER cc_start: 0.8654 (m) cc_final: 0.8337 (t) REVERT: I 674 SER cc_start: 0.8706 (m) cc_final: 0.8435 (t) REVERT: I 709 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7280 (tm-30) REVERT: J 674 SER cc_start: 0.8704 (m) cc_final: 0.8446 (t) REVERT: K 676 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7491 (mt0) REVERT: L 674 SER cc_start: 0.8471 (m) cc_final: 0.8202 (t) REVERT: L 677 GLN cc_start: 0.7847 (mm110) cc_final: 0.7581 (mm-40) outliers start: 1 outliers final: 0 residues processed: 408 average time/residue: 0.1220 time to fit residues: 64.3501 Evaluate side-chains 402 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 GLN A 627 ASN A 706 ASN C 617 GLN C 662 GLN D 642 GLN D 646 ASN ** D 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 610 GLN E 619 GLN E 677 GLN F 603 GLN F 627 ASN ** F 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 696 GLN F 709 GLN ** G 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 619 GLN H 633 GLN H 644 GLN ** H 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 677 GLN H 700 GLN I 617 GLN I 646 ASN I 700 GLN I 706 ASN J 610 GLN J 617 GLN J 646 ASN J 662 GLN J 686 ASN J 700 GLN K 633 GLN K 643 ASN ** K 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 709 GLN L 617 GLN L 619 GLN L 646 ASN ** L 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 677 GLN L 709 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.124379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.108998 restraints weight = 14072.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.112072 restraints weight = 5547.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.113820 restraints weight = 2698.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.114886 restraints weight = 1600.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.115428 restraints weight = 1126.154| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10200 Z= 0.157 Angle : 0.545 8.921 13704 Z= 0.282 Chirality : 0.030 0.176 1548 Planarity : 0.003 0.038 1896 Dihedral : 5.500 83.873 1356 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.37 % Allowed : 15.54 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.55 (0.18), residues: 1272 helix: 3.55 (0.13), residues: 996 sheet: None (None), residues: 0 loop : 0.84 (0.21), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 679 PHE 0.013 0.001 PHE A 675 HIS 0.003 0.001 HIS D 698 Details of bonding type rmsd covalent geometry : bond 0.00315 (10200) covalent geometry : angle 0.54516 (13704) hydrogen bonds : bond 0.05442 ( 1198) hydrogen bonds : angle 3.52150 ( 3594) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 438 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 655 ASN cc_start: 0.9048 (t0) cc_final: 0.8706 (t0) REVERT: A 665 PHE cc_start: 0.9010 (t80) cc_final: 0.8709 (t80) REVERT: A 667 GLU cc_start: 0.7829 (tt0) cc_final: 0.7164 (tt0) REVERT: A 677 GLN cc_start: 0.8603 (tt0) cc_final: 0.8150 (tt0) REVERT: C 616 LEU cc_start: 0.8514 (mp) cc_final: 0.8179 (mp) REVERT: D 674 SER cc_start: 0.9029 (m) cc_final: 0.8648 (t) REVERT: D 688 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7661 (tm-30) REVERT: E 679 ARG cc_start: 0.8014 (tmm-80) cc_final: 0.7673 (tmm-80) REVERT: F 635 ASP cc_start: 0.8628 (t0) cc_final: 0.7994 (t0) REVERT: F 642 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8102 (mm-40) REVERT: F 659 LEU cc_start: 0.8550 (tp) cc_final: 0.7777 (tp) REVERT: F 662 GLN cc_start: 0.6441 (OUTLIER) cc_final: 0.6217 (pm20) REVERT: F 702 MET cc_start: 0.9454 (tpp) cc_final: 0.8985 (tpp) REVERT: G 655 ASN cc_start: 0.9079 (t0) cc_final: 0.8858 (t0) REVERT: G 663 SER cc_start: 0.9049 (t) cc_final: 0.8837 (t) REVERT: G 688 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7612 (tm-30) REVERT: H 635 ASP cc_start: 0.8591 (t70) cc_final: 0.8173 (t70) REVERT: H 674 SER cc_start: 0.9218 (m) cc_final: 0.8834 (t) REVERT: H 709 GLN cc_start: 0.8088 (mm110) cc_final: 0.7402 (tm-30) REVERT: I 674 SER cc_start: 0.9134 (m) cc_final: 0.8828 (t) REVERT: I 699 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8753 (mmmt) REVERT: I 709 GLN cc_start: 0.8576 (mm-40) cc_final: 0.7474 (tm-30) REVERT: J 649 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8124 (mmm-85) REVERT: J 674 SER cc_start: 0.9195 (m) cc_final: 0.8818 (t) REVERT: K 612 GLN cc_start: 0.8074 (mt0) cc_final: 0.7862 (tt0) REVERT: K 642 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8126 (mm-40) REVERT: K 679 ARG cc_start: 0.7752 (tmm-80) cc_final: 0.7466 (tmm-80) REVERT: K 709 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.6342 (tm-30) REVERT: L 604 GLN cc_start: 0.9144 (pm20) cc_final: 0.8861 (pm20) REVERT: L 674 SER cc_start: 0.8974 (m) cc_final: 0.8636 (t) outliers start: 36 outliers final: 12 residues processed: 450 average time/residue: 0.1119 time to fit residues: 65.9752 Evaluate side-chains 445 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 430 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain E residue 630 LEU Chi-restraints excluded: chain E residue 644 GLN Chi-restraints excluded: chain E residue 677 GLN Chi-restraints excluded: chain E residue 699 LYS Chi-restraints excluded: chain F residue 612 GLN Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 662 GLN Chi-restraints excluded: chain I residue 679 ARG Chi-restraints excluded: chain J residue 649 ARG Chi-restraints excluded: chain J residue 662 GLN Chi-restraints excluded: chain K residue 646 ASN Chi-restraints excluded: chain K residue 670 LYS Chi-restraints excluded: chain K residue 699 LYS Chi-restraints excluded: chain K residue 709 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 34 optimal weight: 0.0470 chunk 47 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 GLN C 619 GLN D 619 GLN D 655 ASN ** D 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 677 GLN F 619 GLN F 627 ASN ** F 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 677 GLN G 696 GLN G 698 HIS ** H 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 617 GLN J 617 GLN J 619 GLN ** K 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 676 GLN L 603 GLN L 627 ASN ** L 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.109875 restraints weight = 14017.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.112937 restraints weight = 5521.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.114676 restraints weight = 2701.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115752 restraints weight = 1615.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.116266 restraints weight = 1141.806| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10200 Z= 0.147 Angle : 0.527 9.237 13704 Z= 0.262 Chirality : 0.030 0.153 1548 Planarity : 0.002 0.028 1896 Dihedral : 5.388 84.619 1356 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.68 % Allowed : 19.94 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.86 (0.18), residues: 1272 helix: 4.58 (0.13), residues: 996 sheet: None (None), residues: 0 loop : 0.84 (0.20), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 666 PHE 0.014 0.001 PHE G 675 HIS 0.002 0.001 HIS D 698 Details of bonding type rmsd covalent geometry : bond 0.00283 (10200) covalent geometry : angle 0.52670 (13704) hydrogen bonds : bond 0.05128 ( 1198) hydrogen bonds : angle 3.36959 ( 3594) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 417 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 655 ASN cc_start: 0.9039 (t0) cc_final: 0.8745 (t0) REVERT: A 665 PHE cc_start: 0.8923 (t80) cc_final: 0.8656 (t80) REVERT: B 677 GLN cc_start: 0.8254 (tp-100) cc_final: 0.8048 (tp-100) REVERT: D 674 SER cc_start: 0.9048 (m) cc_final: 0.8678 (t) REVERT: D 688 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7823 (tm-30) REVERT: E 679 ARG cc_start: 0.7948 (tmm-80) cc_final: 0.7517 (tmm-80) REVERT: E 699 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8664 (tmtt) REVERT: F 603 GLN cc_start: 0.6770 (pm20) cc_final: 0.6354 (pm20) REVERT: F 616 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8065 (mm) REVERT: F 642 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8200 (mm-40) REVERT: F 702 MET cc_start: 0.9392 (tpp) cc_final: 0.8852 (tpp) REVERT: G 644 GLN cc_start: 0.8869 (pp30) cc_final: 0.8650 (pp30) REVERT: G 655 ASN cc_start: 0.9051 (t0) cc_final: 0.8764 (t0) REVERT: G 663 SER cc_start: 0.9083 (t) cc_final: 0.8869 (t) REVERT: G 688 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7616 (tm-30) REVERT: H 635 ASP cc_start: 0.8623 (t70) cc_final: 0.8219 (t70) REVERT: H 665 PHE cc_start: 0.8924 (t80) cc_final: 0.8480 (t80) REVERT: H 674 SER cc_start: 0.9165 (m) cc_final: 0.8803 (t) REVERT: H 709 GLN cc_start: 0.8286 (mm110) cc_final: 0.7347 (tm-30) REVERT: I 644 GLN cc_start: 0.8601 (pp30) cc_final: 0.7939 (pp30) REVERT: I 674 SER cc_start: 0.9129 (m) cc_final: 0.8810 (t) REVERT: I 699 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8656 (mmmt) REVERT: I 709 GLN cc_start: 0.8539 (mm-40) cc_final: 0.7455 (tm-30) REVERT: J 649 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8092 (mmm-85) REVERT: J 665 PHE cc_start: 0.9017 (t80) cc_final: 0.8701 (t80) REVERT: J 674 SER cc_start: 0.9198 (m) cc_final: 0.8815 (t) REVERT: K 642 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8129 (mm-40) REVERT: K 669 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8952 (tt) REVERT: K 676 GLN cc_start: 0.8573 (tt0) cc_final: 0.7859 (tt0) REVERT: K 679 ARG cc_start: 0.8020 (tmm-80) cc_final: 0.7514 (tmm-80) REVERT: L 642 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: L 674 SER cc_start: 0.8924 (m) cc_final: 0.8602 (t) REVERT: L 681 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8063 (tm-30) outliers start: 50 outliers final: 24 residues processed: 430 average time/residue: 0.1154 time to fit residues: 64.7684 Evaluate side-chains 429 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 400 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 679 ARG Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain D residue 650 ILE Chi-restraints excluded: chain E residue 630 LEU Chi-restraints excluded: chain E residue 677 GLN Chi-restraints excluded: chain E residue 699 LYS Chi-restraints excluded: chain F residue 616 LEU Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain G residue 664 GLU Chi-restraints excluded: chain G residue 679 ARG Chi-restraints excluded: chain G residue 696 GLN Chi-restraints excluded: chain H residue 677 GLN Chi-restraints excluded: chain H residue 688 GLU Chi-restraints excluded: chain I residue 679 ARG Chi-restraints excluded: chain J residue 632 LEU Chi-restraints excluded: chain J residue 649 ARG Chi-restraints excluded: chain K residue 646 ASN Chi-restraints excluded: chain K residue 659 LEU Chi-restraints excluded: chain K residue 669 LEU Chi-restraints excluded: chain K residue 670 LYS Chi-restraints excluded: chain K residue 681 GLU Chi-restraints excluded: chain K residue 692 LYS Chi-restraints excluded: chain K residue 699 LYS Chi-restraints excluded: chain L residue 632 LEU Chi-restraints excluded: chain L residue 642 GLN Chi-restraints excluded: chain L residue 670 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 89 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 GLN B 619 GLN D 619 GLN ** D 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 619 GLN E 677 GLN F 619 GLN F 677 GLN G 619 GLN ** G 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 696 GLN G 698 HIS H 603 GLN ** H 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 610 GLN J 619 GLN J 662 GLN ** K 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 603 GLN L 627 ASN ** L 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 677 GLN L 696 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.110617 restraints weight = 14117.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113299 restraints weight = 5785.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114838 restraints weight = 2919.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115710 restraints weight = 1809.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.116133 restraints weight = 1346.800| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10200 Z= 0.157 Angle : 0.541 9.623 13704 Z= 0.271 Chirality : 0.031 0.158 1548 Planarity : 0.002 0.020 1896 Dihedral : 5.327 87.505 1356 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.18 % Allowed : 19.38 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 7.37 (0.17), residues: 1272 helix: 4.90 (0.11), residues: 1224 sheet: None (None), residues: 0 loop : -0.80 (0.54), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 666 PHE 0.013 0.001 PHE I 675 HIS 0.002 0.001 HIS B 698 Details of bonding type rmsd covalent geometry : bond 0.00324 (10200) covalent geometry : angle 0.54091 (13704) hydrogen bonds : bond 0.05015 ( 1198) hydrogen bonds : angle 3.39845 ( 3594) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 422 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 ASP cc_start: 0.8621 (t0) cc_final: 0.8086 (t0) REVERT: A 655 ASN cc_start: 0.9106 (t0) cc_final: 0.8805 (t0) REVERT: A 662 GLN cc_start: 0.6709 (pt0) cc_final: 0.6476 (pt0) REVERT: C 665 PHE cc_start: 0.8808 (t80) cc_final: 0.8581 (t80) REVERT: D 603 GLN cc_start: 0.3375 (mp10) cc_final: 0.1342 (mp10) REVERT: D 674 SER cc_start: 0.9059 (m) cc_final: 0.8652 (t) REVERT: D 688 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7741 (tm-30) REVERT: E 655 ASN cc_start: 0.9018 (t0) cc_final: 0.8404 (t0) REVERT: E 679 ARG cc_start: 0.7840 (tmm-80) cc_final: 0.7371 (tmm-80) REVERT: E 699 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8706 (tmtt) REVERT: F 616 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7950 (mm) REVERT: F 635 ASP cc_start: 0.8643 (t0) cc_final: 0.8071 (t0) REVERT: F 665 PHE cc_start: 0.8943 (t80) cc_final: 0.8639 (t80) REVERT: F 702 MET cc_start: 0.9394 (tpp) cc_final: 0.8782 (tpp) REVERT: G 644 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8563 (pp30) REVERT: G 655 ASN cc_start: 0.9085 (t0) cc_final: 0.8819 (t0) REVERT: G 663 SER cc_start: 0.9225 (t) cc_final: 0.8950 (t) REVERT: G 688 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7579 (tm-30) REVERT: H 635 ASP cc_start: 0.8594 (t70) cc_final: 0.8212 (t70) REVERT: H 674 SER cc_start: 0.9098 (m) cc_final: 0.8717 (t) REVERT: H 709 GLN cc_start: 0.8205 (mm110) cc_final: 0.7235 (tm-30) REVERT: I 644 GLN cc_start: 0.8563 (pp30) cc_final: 0.7968 (pp30) REVERT: I 674 SER cc_start: 0.9049 (m) cc_final: 0.8760 (t) REVERT: I 699 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8707 (mmmt) REVERT: I 709 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7361 (tm-30) REVERT: J 655 ASN cc_start: 0.8870 (t0) cc_final: 0.8414 (t0) REVERT: J 674 SER cc_start: 0.9164 (m) cc_final: 0.8818 (t) REVERT: K 676 GLN cc_start: 0.8323 (tt0) cc_final: 0.7649 (mt0) REVERT: K 677 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8010 (tp40) REVERT: K 679 ARG cc_start: 0.7915 (tmm-80) cc_final: 0.7588 (tmm-80) REVERT: L 674 SER cc_start: 0.8920 (m) cc_final: 0.8591 (t) REVERT: L 681 GLU cc_start: 0.8559 (mm-30) cc_final: 0.7972 (tm-30) REVERT: L 692 LYS cc_start: 0.8853 (ttpt) cc_final: 0.8396 (ttpt) outliers start: 66 outliers final: 35 residues processed: 442 average time/residue: 0.1179 time to fit residues: 68.1797 Evaluate side-chains 456 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 417 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 679 ARG Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain D residue 650 ILE Chi-restraints excluded: chain E residue 630 LEU Chi-restraints excluded: chain E residue 699 LYS Chi-restraints excluded: chain F residue 604 GLN Chi-restraints excluded: chain F residue 616 LEU Chi-restraints excluded: chain F residue 658 ASP Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain G residue 644 GLN Chi-restraints excluded: chain G residue 664 GLU Chi-restraints excluded: chain G residue 672 VAL Chi-restraints excluded: chain H residue 662 GLN Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain H residue 677 GLN Chi-restraints excluded: chain H residue 688 GLU Chi-restraints excluded: chain I residue 659 LEU Chi-restraints excluded: chain I residue 679 ARG Chi-restraints excluded: chain J residue 632 LEU Chi-restraints excluded: chain J residue 659 LEU Chi-restraints excluded: chain J residue 662 GLN Chi-restraints excluded: chain K residue 646 ASN Chi-restraints excluded: chain K residue 659 LEU Chi-restraints excluded: chain K residue 670 LYS Chi-restraints excluded: chain K residue 672 VAL Chi-restraints excluded: chain K residue 677 GLN Chi-restraints excluded: chain K residue 681 GLU Chi-restraints excluded: chain K residue 688 GLU Chi-restraints excluded: chain K residue 692 LYS Chi-restraints excluded: chain K residue 699 LYS Chi-restraints excluded: chain L residue 659 LEU Chi-restraints excluded: chain L residue 664 GLU Chi-restraints excluded: chain L residue 669 LEU Chi-restraints excluded: chain L residue 670 LYS Chi-restraints excluded: chain L residue 672 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 GLN B 619 GLN B 677 GLN C 619 GLN F 619 GLN ** G 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 698 HIS H 603 GLN ** H 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 627 ASN J 610 GLN J 662 GLN J 696 GLN ** K 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 603 GLN L 627 ASN ** L 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 677 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.126225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110660 restraints weight = 13964.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.113521 restraints weight = 5655.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.115118 restraints weight = 2845.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116081 restraints weight = 1756.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.116546 restraints weight = 1283.730| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10200 Z= 0.154 Angle : 0.551 10.080 13704 Z= 0.272 Chirality : 0.030 0.153 1548 Planarity : 0.002 0.016 1896 Dihedral : 5.249 88.078 1356 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.15 % Allowed : 22.00 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 7.49 (0.17), residues: 1272 helix: 4.98 (0.11), residues: 1224 sheet: None (None), residues: 0 loop : -0.83 (0.51), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 666 PHE 0.012 0.001 PHE I 675 HIS 0.002 0.001 HIS B 698 Details of bonding type rmsd covalent geometry : bond 0.00320 (10200) covalent geometry : angle 0.55116 (13704) hydrogen bonds : bond 0.04935 ( 1198) hydrogen bonds : angle 3.37157 ( 3594) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 425 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 ASP cc_start: 0.8650 (t0) cc_final: 0.8094 (t0) REVERT: A 655 ASN cc_start: 0.9090 (t0) cc_final: 0.8755 (t0) REVERT: B 703 ASP cc_start: 0.8928 (m-30) cc_final: 0.8615 (m-30) REVERT: D 603 GLN cc_start: 0.3596 (mp10) cc_final: 0.3069 (mp10) REVERT: D 674 SER cc_start: 0.9116 (m) cc_final: 0.8774 (t) REVERT: D 688 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7841 (tm-30) REVERT: E 679 ARG cc_start: 0.7876 (tmm-80) cc_final: 0.7297 (tmm-80) REVERT: E 699 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8692 (tmtt) REVERT: F 616 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7946 (mm) REVERT: F 635 ASP cc_start: 0.8671 (t0) cc_final: 0.8083 (t0) REVERT: F 702 MET cc_start: 0.9342 (tpp) cc_final: 0.8638 (tpp) REVERT: G 644 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8519 (pp30) REVERT: G 655 ASN cc_start: 0.9054 (t0) cc_final: 0.8780 (t0) REVERT: G 688 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7671 (tm-30) REVERT: H 635 ASP cc_start: 0.8673 (t70) cc_final: 0.8243 (t70) REVERT: H 655 ASN cc_start: 0.8701 (t0) cc_final: 0.8454 (t0) REVERT: H 674 SER cc_start: 0.9109 (m) cc_final: 0.8758 (t) REVERT: H 709 GLN cc_start: 0.8264 (mm110) cc_final: 0.7159 (tm-30) REVERT: I 644 GLN cc_start: 0.8567 (pp30) cc_final: 0.8005 (pp30) REVERT: I 674 SER cc_start: 0.9024 (m) cc_final: 0.8767 (t) REVERT: I 699 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8679 (mmmt) REVERT: I 709 GLN cc_start: 0.8449 (mm-40) cc_final: 0.7367 (tm-30) REVERT: J 655 ASN cc_start: 0.8878 (t0) cc_final: 0.8413 (t0) REVERT: J 674 SER cc_start: 0.9096 (m) cc_final: 0.8779 (t) REVERT: K 676 GLN cc_start: 0.8309 (tt0) cc_final: 0.7596 (mt0) REVERT: K 679 ARG cc_start: 0.8027 (tmm-80) cc_final: 0.7618 (tmm-80) REVERT: L 642 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.6853 (tm-30) REVERT: L 674 SER cc_start: 0.8684 (m) cc_final: 0.8422 (t) REVERT: L 681 GLU cc_start: 0.8628 (mm-30) cc_final: 0.7996 (tm-30) REVERT: L 692 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8405 (ttpt) outliers start: 55 outliers final: 35 residues processed: 437 average time/residue: 0.1138 time to fit residues: 64.9854 Evaluate side-chains 463 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 424 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain E residue 670 LYS Chi-restraints excluded: chain E residue 699 LYS Chi-restraints excluded: chain F residue 604 GLN Chi-restraints excluded: chain F residue 616 LEU Chi-restraints excluded: chain F residue 658 ASP Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain G residue 644 GLN Chi-restraints excluded: chain G residue 664 GLU Chi-restraints excluded: chain G residue 672 VAL Chi-restraints excluded: chain H residue 662 GLN Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain H residue 677 GLN Chi-restraints excluded: chain H residue 679 ARG Chi-restraints excluded: chain H residue 688 GLU Chi-restraints excluded: chain I residue 659 LEU Chi-restraints excluded: chain I residue 672 VAL Chi-restraints excluded: chain J residue 632 LEU Chi-restraints excluded: chain J residue 659 LEU Chi-restraints excluded: chain J residue 662 GLN Chi-restraints excluded: chain K residue 638 LYS Chi-restraints excluded: chain K residue 646 ASN Chi-restraints excluded: chain K residue 659 LEU Chi-restraints excluded: chain K residue 670 LYS Chi-restraints excluded: chain K residue 672 VAL Chi-restraints excluded: chain K residue 681 GLU Chi-restraints excluded: chain K residue 688 GLU Chi-restraints excluded: chain K residue 692 LYS Chi-restraints excluded: chain K residue 699 LYS Chi-restraints excluded: chain L residue 642 GLN Chi-restraints excluded: chain L residue 664 GLU Chi-restraints excluded: chain L residue 669 LEU Chi-restraints excluded: chain L residue 670 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 90 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 619 GLN ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 GLN ** G 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 698 HIS H 603 GLN ** H 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 677 GLN I 627 ASN J 610 GLN J 662 GLN J 696 GLN ** K 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 603 GLN L 627 ASN ** L 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 677 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107025 restraints weight = 14474.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.109752 restraints weight = 5950.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111295 restraints weight = 3019.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112144 restraints weight = 1867.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112686 restraints weight = 1400.052| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10200 Z= 0.198 Angle : 0.625 12.480 13704 Z= 0.310 Chirality : 0.034 0.176 1548 Planarity : 0.002 0.018 1896 Dihedral : 5.129 76.745 1356 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 5.99 % Allowed : 24.63 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 7.20 (0.17), residues: 1272 helix: 4.69 (0.11), residues: 1248 sheet: None (None), residues: 0 loop : -0.86 (0.71), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 666 PHE 0.014 0.002 PHE I 675 HIS 0.003 0.001 HIS B 698 Details of bonding type rmsd covalent geometry : bond 0.00427 (10200) covalent geometry : angle 0.62516 (13704) hydrogen bonds : bond 0.05155 ( 1198) hydrogen bonds : angle 3.57280 ( 3594) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 452 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 655 ASN cc_start: 0.9137 (t0) cc_final: 0.8838 (t0) REVERT: A 677 GLN cc_start: 0.8473 (tt0) cc_final: 0.7921 (tm-30) REVERT: B 655 ASN cc_start: 0.9015 (t0) cc_final: 0.8558 (t0) REVERT: B 703 ASP cc_start: 0.8895 (m-30) cc_final: 0.8573 (m-30) REVERT: C 655 ASN cc_start: 0.9017 (t0) cc_final: 0.8487 (t0) REVERT: D 674 SER cc_start: 0.9138 (m) cc_final: 0.8789 (t) REVERT: D 688 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7864 (tm-30) REVERT: E 635 ASP cc_start: 0.8654 (t0) cc_final: 0.8150 (t0) REVERT: E 655 ASN cc_start: 0.9037 (t0) cc_final: 0.8465 (t0) REVERT: E 679 ARG cc_start: 0.7889 (tmm-80) cc_final: 0.7308 (tmm-80) REVERT: E 699 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8624 (tmtt) REVERT: F 616 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8052 (mm) REVERT: F 659 LEU cc_start: 0.8675 (tp) cc_final: 0.7862 (tp) REVERT: F 662 GLN cc_start: 0.6561 (OUTLIER) cc_final: 0.6288 (pm20) REVERT: F 702 MET cc_start: 0.9249 (tpp) cc_final: 0.8522 (tpp) REVERT: G 644 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8591 (pp30) REVERT: G 655 ASN cc_start: 0.9106 (t0) cc_final: 0.8862 (t0) REVERT: G 688 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7799 (tm-30) REVERT: H 635 ASP cc_start: 0.8723 (t70) cc_final: 0.8200 (t0) REVERT: H 655 ASN cc_start: 0.8797 (t0) cc_final: 0.8546 (t0) REVERT: H 666 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6368 (mpp80) REVERT: H 674 SER cc_start: 0.9122 (m) cc_final: 0.8728 (t) REVERT: H 709 GLN cc_start: 0.8397 (mm110) cc_final: 0.7213 (tm-30) REVERT: I 644 GLN cc_start: 0.8665 (pp30) cc_final: 0.8246 (pp30) REVERT: I 674 SER cc_start: 0.9096 (m) cc_final: 0.8780 (t) REVERT: I 699 LYS cc_start: 0.9037 (mmmt) cc_final: 0.8615 (mmmt) REVERT: I 709 GLN cc_start: 0.8453 (mm-40) cc_final: 0.7376 (tm-30) REVERT: J 655 ASN cc_start: 0.8928 (t0) cc_final: 0.8459 (t0) REVERT: J 674 SER cc_start: 0.9194 (m) cc_final: 0.8837 (t) REVERT: J 681 GLU cc_start: 0.8531 (tp30) cc_final: 0.8193 (tp30) REVERT: K 676 GLN cc_start: 0.8324 (tt0) cc_final: 0.7594 (mt0) REVERT: K 679 ARG cc_start: 0.8073 (tmm-80) cc_final: 0.7781 (tmm-80) REVERT: L 674 SER cc_start: 0.8733 (m) cc_final: 0.8483 (t) REVERT: L 681 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8026 (tm-30) REVERT: L 692 LYS cc_start: 0.8823 (ttpt) cc_final: 0.8379 (ttpt) outliers start: 64 outliers final: 41 residues processed: 471 average time/residue: 0.1101 time to fit residues: 68.0985 Evaluate side-chains 483 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 437 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain E residue 670 LYS Chi-restraints excluded: chain E residue 692 LYS Chi-restraints excluded: chain E residue 699 LYS Chi-restraints excluded: chain F residue 616 LEU Chi-restraints excluded: chain F residue 658 ASP Chi-restraints excluded: chain F residue 662 GLN Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain G residue 614 VAL Chi-restraints excluded: chain G residue 644 GLN Chi-restraints excluded: chain G residue 664 GLU Chi-restraints excluded: chain G residue 672 VAL Chi-restraints excluded: chain H residue 603 GLN Chi-restraints excluded: chain H residue 666 ARG Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain H residue 688 GLU Chi-restraints excluded: chain I residue 638 LYS Chi-restraints excluded: chain I residue 659 LEU Chi-restraints excluded: chain I residue 672 VAL Chi-restraints excluded: chain I residue 679 ARG Chi-restraints excluded: chain J residue 614 VAL Chi-restraints excluded: chain J residue 632 LEU Chi-restraints excluded: chain J residue 659 LEU Chi-restraints excluded: chain J residue 662 GLN Chi-restraints excluded: chain J residue 672 VAL Chi-restraints excluded: chain J residue 704 ILE Chi-restraints excluded: chain K residue 639 VAL Chi-restraints excluded: chain K residue 646 ASN Chi-restraints excluded: chain K residue 659 LEU Chi-restraints excluded: chain K residue 670 LYS Chi-restraints excluded: chain K residue 672 VAL Chi-restraints excluded: chain K residue 681 GLU Chi-restraints excluded: chain K residue 688 GLU Chi-restraints excluded: chain K residue 692 LYS Chi-restraints excluded: chain K residue 699 LYS Chi-restraints excluded: chain L residue 664 GLU Chi-restraints excluded: chain L residue 669 LEU Chi-restraints excluded: chain L residue 670 LYS Chi-restraints excluded: chain L residue 672 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 110 optimal weight: 0.0570 chunk 14 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 GLN C 700 GLN ** G 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 603 GLN H 619 GLN ** H 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 662 GLN H 677 GLN I 627 ASN J 610 GLN J 662 GLN K 619 GLN K 643 ASN K 646 ASN L 603 GLN L 627 ASN ** L 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 677 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.125935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.110606 restraints weight = 13877.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113382 restraints weight = 5624.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114927 restraints weight = 2809.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115818 restraints weight = 1727.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.116344 restraints weight = 1269.916| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10200 Z= 0.148 Angle : 0.579 11.004 13704 Z= 0.280 Chirality : 0.030 0.146 1548 Planarity : 0.002 0.017 1896 Dihedral : 4.874 70.415 1356 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.12 % Allowed : 27.90 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 7.66 (0.17), residues: 1272 helix: 4.98 (0.11), residues: 1248 sheet: None (None), residues: 0 loop : -0.87 (0.78), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 666 PHE 0.008 0.001 PHE E 675 HIS 0.002 0.001 HIS G 698 Details of bonding type rmsd covalent geometry : bond 0.00302 (10200) covalent geometry : angle 0.57860 (13704) hydrogen bonds : bond 0.04954 ( 1198) hydrogen bonds : angle 3.33247 ( 3594) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 426 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 ASP cc_start: 0.8648 (t0) cc_final: 0.8076 (t0) REVERT: A 655 ASN cc_start: 0.9093 (t0) cc_final: 0.8787 (t0) REVERT: B 655 ASN cc_start: 0.9014 (t0) cc_final: 0.8528 (t0) REVERT: B 703 ASP cc_start: 0.8920 (m-30) cc_final: 0.8613 (m-30) REVERT: D 674 SER cc_start: 0.9194 (m) cc_final: 0.8769 (t) REVERT: D 688 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7925 (tm-30) REVERT: D 699 LYS cc_start: 0.8854 (tppt) cc_final: 0.8581 (tppt) REVERT: E 679 ARG cc_start: 0.7913 (tmm-80) cc_final: 0.7297 (tmm-80) REVERT: E 699 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8614 (tmtt) REVERT: F 659 LEU cc_start: 0.8595 (tp) cc_final: 0.7769 (tp) REVERT: F 702 MET cc_start: 0.9210 (tpp) cc_final: 0.8463 (tpp) REVERT: G 644 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8384 (pp30) REVERT: G 655 ASN cc_start: 0.9059 (t0) cc_final: 0.8811 (t0) REVERT: G 688 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7769 (tm-30) REVERT: H 603 GLN cc_start: 0.6597 (OUTLIER) cc_final: 0.6217 (pm20) REVERT: H 635 ASP cc_start: 0.8750 (t70) cc_final: 0.8204 (t0) REVERT: H 655 ASN cc_start: 0.8694 (t0) cc_final: 0.8476 (t0) REVERT: H 674 SER cc_start: 0.9099 (m) cc_final: 0.8746 (t) REVERT: H 709 GLN cc_start: 0.8317 (mm110) cc_final: 0.7171 (tm-30) REVERT: I 644 GLN cc_start: 0.8619 (pp30) cc_final: 0.8275 (pp30) REVERT: I 674 SER cc_start: 0.9019 (m) cc_final: 0.8737 (t) REVERT: I 699 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8624 (mmmt) REVERT: I 709 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7388 (tm-30) REVERT: J 655 ASN cc_start: 0.8865 (t0) cc_final: 0.8403 (t0) REVERT: J 674 SER cc_start: 0.9118 (m) cc_final: 0.8772 (t) REVERT: J 681 GLU cc_start: 0.8497 (tp30) cc_final: 0.8113 (tp30) REVERT: K 676 GLN cc_start: 0.8327 (tt0) cc_final: 0.7586 (mt0) REVERT: K 679 ARG cc_start: 0.8068 (tmm-80) cc_final: 0.7804 (tmm-80) REVERT: L 642 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: L 645 LEU cc_start: 0.8621 (tt) cc_final: 0.8219 (tp) REVERT: L 674 SER cc_start: 0.8762 (m) cc_final: 0.8505 (t) REVERT: L 681 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8023 (tm-30) outliers start: 44 outliers final: 30 residues processed: 437 average time/residue: 0.1167 time to fit residues: 66.8303 Evaluate side-chains 450 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 416 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain E residue 670 LYS Chi-restraints excluded: chain E residue 699 LYS Chi-restraints excluded: chain F residue 632 LEU Chi-restraints excluded: chain F residue 658 ASP Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain G residue 644 GLN Chi-restraints excluded: chain G residue 664 GLU Chi-restraints excluded: chain H residue 603 GLN Chi-restraints excluded: chain H residue 632 LEU Chi-restraints excluded: chain H residue 679 ARG Chi-restraints excluded: chain H residue 688 GLU Chi-restraints excluded: chain I residue 659 LEU Chi-restraints excluded: chain J residue 632 LEU Chi-restraints excluded: chain J residue 659 LEU Chi-restraints excluded: chain J residue 662 GLN Chi-restraints excluded: chain K residue 638 LYS Chi-restraints excluded: chain K residue 639 VAL Chi-restraints excluded: chain K residue 659 LEU Chi-restraints excluded: chain K residue 670 LYS Chi-restraints excluded: chain K residue 681 GLU Chi-restraints excluded: chain K residue 688 GLU Chi-restraints excluded: chain K residue 692 LYS Chi-restraints excluded: chain L residue 603 GLN Chi-restraints excluded: chain L residue 642 GLN Chi-restraints excluded: chain L residue 664 GLU Chi-restraints excluded: chain L residue 669 LEU Chi-restraints excluded: chain L residue 670 LYS Chi-restraints excluded: chain L residue 672 VAL Chi-restraints excluded: chain L residue 679 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 29 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 619 GLN ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 GLN ** G 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 603 GLN ** H 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 610 GLN L 603 GLN L 627 ASN ** L 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 677 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.109901 restraints weight = 14054.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.112653 restraints weight = 5677.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.114236 restraints weight = 2832.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.115095 restraints weight = 1724.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.115620 restraints weight = 1276.572| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10200 Z= 0.158 Angle : 0.624 11.760 13704 Z= 0.295 Chirality : 0.031 0.147 1548 Planarity : 0.002 0.019 1896 Dihedral : 4.747 65.433 1356 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.59 % Allowed : 28.00 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 7.67 (0.17), residues: 1272 helix: 4.98 (0.11), residues: 1248 sheet: None (None), residues: 0 loop : -0.77 (0.82), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 666 PHE 0.014 0.001 PHE E 675 HIS 0.002 0.001 HIS G 698 Details of bonding type rmsd covalent geometry : bond 0.00333 (10200) covalent geometry : angle 0.62366 (13704) hydrogen bonds : bond 0.04890 ( 1198) hydrogen bonds : angle 3.37505 ( 3594) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 429 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 ASP cc_start: 0.8723 (t0) cc_final: 0.8148 (t0) REVERT: A 655 ASN cc_start: 0.9102 (t0) cc_final: 0.8813 (t0) REVERT: A 677 GLN cc_start: 0.8476 (tt0) cc_final: 0.7827 (tm-30) REVERT: B 655 ASN cc_start: 0.9022 (t0) cc_final: 0.8549 (t0) REVERT: B 703 ASP cc_start: 0.8938 (m-30) cc_final: 0.8658 (m-30) REVERT: C 655 ASN cc_start: 0.8974 (t0) cc_final: 0.8423 (t0) REVERT: D 674 SER cc_start: 0.9225 (m) cc_final: 0.8805 (t) REVERT: D 688 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7936 (tm-30) REVERT: D 699 LYS cc_start: 0.8862 (tppt) cc_final: 0.8583 (tppt) REVERT: E 635 ASP cc_start: 0.8636 (t0) cc_final: 0.8133 (t0) REVERT: E 679 ARG cc_start: 0.7933 (tmm-80) cc_final: 0.7367 (tmm-80) REVERT: E 699 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8695 (tmtt) REVERT: F 616 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8033 (mm) REVERT: F 702 MET cc_start: 0.9206 (tpp) cc_final: 0.8466 (tpp) REVERT: G 644 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8395 (pp30) REVERT: G 655 ASN cc_start: 0.9063 (t0) cc_final: 0.8748 (t0) REVERT: G 688 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7794 (tm-30) REVERT: H 635 ASP cc_start: 0.8732 (t70) cc_final: 0.8350 (t70) REVERT: H 655 ASN cc_start: 0.8744 (t0) cc_final: 0.8504 (t0) REVERT: H 666 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6675 (mpp80) REVERT: H 674 SER cc_start: 0.9051 (m) cc_final: 0.8696 (t) REVERT: H 709 GLN cc_start: 0.8329 (mm110) cc_final: 0.7168 (tm-30) REVERT: I 644 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8331 (pp30) REVERT: I 674 SER cc_start: 0.9024 (m) cc_final: 0.8741 (t) REVERT: I 677 GLN cc_start: 0.8248 (tp40) cc_final: 0.8031 (tp40) REVERT: I 699 LYS cc_start: 0.9031 (mmmt) cc_final: 0.8654 (mmmt) REVERT: I 709 GLN cc_start: 0.8417 (mm-40) cc_final: 0.7387 (tm-30) REVERT: J 655 ASN cc_start: 0.8871 (t0) cc_final: 0.8433 (t0) REVERT: J 674 SER cc_start: 0.9134 (m) cc_final: 0.8787 (t) REVERT: J 681 GLU cc_start: 0.8512 (tp30) cc_final: 0.8128 (tp30) REVERT: K 676 GLN cc_start: 0.8334 (tt0) cc_final: 0.7505 (mt0) REVERT: K 679 ARG cc_start: 0.8108 (tmm-80) cc_final: 0.7827 (tmm-80) REVERT: L 642 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: L 674 SER cc_start: 0.8771 (m) cc_final: 0.8509 (t) REVERT: L 681 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8024 (tm-30) outliers start: 49 outliers final: 34 residues processed: 442 average time/residue: 0.1150 time to fit residues: 66.3392 Evaluate side-chains 474 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 434 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain E residue 670 LYS Chi-restraints excluded: chain E residue 674 SER Chi-restraints excluded: chain E residue 699 LYS Chi-restraints excluded: chain F residue 604 GLN Chi-restraints excluded: chain F residue 616 LEU Chi-restraints excluded: chain F residue 622 LEU Chi-restraints excluded: chain F residue 632 LEU Chi-restraints excluded: chain F residue 658 ASP Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain G residue 644 GLN Chi-restraints excluded: chain G residue 664 GLU Chi-restraints excluded: chain H residue 603 GLN Chi-restraints excluded: chain H residue 632 LEU Chi-restraints excluded: chain H residue 666 ARG Chi-restraints excluded: chain H residue 679 ARG Chi-restraints excluded: chain H residue 688 GLU Chi-restraints excluded: chain I residue 644 GLN Chi-restraints excluded: chain I residue 659 LEU Chi-restraints excluded: chain J residue 632 LEU Chi-restraints excluded: chain J residue 659 LEU Chi-restraints excluded: chain K residue 638 LYS Chi-restraints excluded: chain K residue 639 VAL Chi-restraints excluded: chain K residue 659 LEU Chi-restraints excluded: chain K residue 670 LYS Chi-restraints excluded: chain K residue 681 GLU Chi-restraints excluded: chain K residue 688 GLU Chi-restraints excluded: chain K residue 692 LYS Chi-restraints excluded: chain K residue 699 LYS Chi-restraints excluded: chain L residue 603 GLN Chi-restraints excluded: chain L residue 642 GLN Chi-restraints excluded: chain L residue 669 LEU Chi-restraints excluded: chain L residue 672 VAL Chi-restraints excluded: chain L residue 679 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 72 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 GLN ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 603 GLN ** H 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 610 GLN J 662 GLN K 646 ASN L 603 GLN ** L 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 677 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.109802 restraints weight = 14072.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112527 restraints weight = 5677.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.114094 restraints weight = 2831.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114908 restraints weight = 1724.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.115416 restraints weight = 1284.003| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10200 Z= 0.156 Angle : 0.632 12.710 13704 Z= 0.298 Chirality : 0.030 0.143 1548 Planarity : 0.002 0.019 1896 Dihedral : 4.608 62.834 1356 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.21 % Allowed : 28.37 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 7.76 (0.17), residues: 1272 helix: 5.04 (0.10), residues: 1248 sheet: None (None), residues: 0 loop : -0.86 (0.90), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 666 PHE 0.014 0.001 PHE E 675 HIS 0.002 0.001 HIS G 698 Details of bonding type rmsd covalent geometry : bond 0.00328 (10200) covalent geometry : angle 0.63244 (13704) hydrogen bonds : bond 0.04863 ( 1198) hydrogen bonds : angle 3.35713 ( 3594) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 430 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 ASP cc_start: 0.8710 (t0) cc_final: 0.8113 (t0) REVERT: A 655 ASN cc_start: 0.9103 (t0) cc_final: 0.8820 (t0) REVERT: B 642 GLN cc_start: 0.8488 (mm110) cc_final: 0.8190 (tt0) REVERT: B 655 ASN cc_start: 0.9036 (t0) cc_final: 0.8563 (t0) REVERT: B 703 ASP cc_start: 0.8933 (m-30) cc_final: 0.8649 (m-30) REVERT: C 655 ASN cc_start: 0.8979 (t0) cc_final: 0.8409 (t0) REVERT: D 674 SER cc_start: 0.9198 (m) cc_final: 0.8768 (t) REVERT: D 688 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7928 (tm-30) REVERT: D 699 LYS cc_start: 0.8863 (tppt) cc_final: 0.8579 (tppt) REVERT: E 679 ARG cc_start: 0.7927 (tmm-80) cc_final: 0.7403 (tmm-80) REVERT: E 699 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8750 (tmtt) REVERT: F 616 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8023 (mm) REVERT: F 702 MET cc_start: 0.9256 (tpp) cc_final: 0.8502 (tpp) REVERT: G 644 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8403 (pp30) REVERT: G 655 ASN cc_start: 0.9061 (t0) cc_final: 0.8776 (t0) REVERT: G 688 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7780 (tm-30) REVERT: H 603 GLN cc_start: 0.6377 (OUTLIER) cc_final: 0.6115 (pm20) REVERT: H 635 ASP cc_start: 0.8721 (t70) cc_final: 0.8340 (t70) REVERT: H 644 GLN cc_start: 0.8310 (mm-40) cc_final: 0.8078 (mm110) REVERT: H 655 ASN cc_start: 0.8759 (t0) cc_final: 0.8533 (t0) REVERT: H 666 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6715 (mpp80) REVERT: H 674 SER cc_start: 0.9052 (m) cc_final: 0.8671 (t) REVERT: H 709 GLN cc_start: 0.8289 (mm110) cc_final: 0.7135 (tm-30) REVERT: I 644 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8348 (pp30) REVERT: I 674 SER cc_start: 0.9023 (m) cc_final: 0.8737 (t) REVERT: I 699 LYS cc_start: 0.9057 (mmmt) cc_final: 0.8662 (mmmt) REVERT: I 709 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7374 (tm-30) REVERT: J 655 ASN cc_start: 0.8856 (t0) cc_final: 0.8397 (t0) REVERT: J 662 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6692 (pt0) REVERT: J 674 SER cc_start: 0.9126 (m) cc_final: 0.8771 (t) REVERT: J 681 GLU cc_start: 0.8540 (tp30) cc_final: 0.8136 (tp30) REVERT: K 676 GLN cc_start: 0.8358 (tt0) cc_final: 0.7560 (mt0) REVERT: K 679 ARG cc_start: 0.8101 (tmm-80) cc_final: 0.7826 (tmm-80) REVERT: L 642 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: L 674 SER cc_start: 0.8760 (m) cc_final: 0.8505 (t) REVERT: L 681 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8025 (tm-30) outliers start: 45 outliers final: 35 residues processed: 442 average time/residue: 0.1149 time to fit residues: 66.4020 Evaluate side-chains 471 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 428 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain E residue 670 LYS Chi-restraints excluded: chain E residue 674 SER Chi-restraints excluded: chain E residue 699 LYS Chi-restraints excluded: chain F residue 616 LEU Chi-restraints excluded: chain F residue 622 LEU Chi-restraints excluded: chain F residue 632 LEU Chi-restraints excluded: chain F residue 658 ASP Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 710 SER Chi-restraints excluded: chain G residue 644 GLN Chi-restraints excluded: chain G residue 664 GLU Chi-restraints excluded: chain H residue 603 GLN Chi-restraints excluded: chain H residue 632 LEU Chi-restraints excluded: chain H residue 666 ARG Chi-restraints excluded: chain H residue 679 ARG Chi-restraints excluded: chain H residue 688 GLU Chi-restraints excluded: chain H residue 692 LYS Chi-restraints excluded: chain I residue 644 GLN Chi-restraints excluded: chain I residue 659 LEU Chi-restraints excluded: chain J residue 632 LEU Chi-restraints excluded: chain J residue 659 LEU Chi-restraints excluded: chain J residue 662 GLN Chi-restraints excluded: chain J residue 672 VAL Chi-restraints excluded: chain K residue 639 VAL Chi-restraints excluded: chain K residue 646 ASN Chi-restraints excluded: chain K residue 659 LEU Chi-restraints excluded: chain K residue 670 LYS Chi-restraints excluded: chain K residue 681 GLU Chi-restraints excluded: chain K residue 688 GLU Chi-restraints excluded: chain K residue 692 LYS Chi-restraints excluded: chain K residue 699 LYS Chi-restraints excluded: chain L residue 603 GLN Chi-restraints excluded: chain L residue 642 GLN Chi-restraints excluded: chain L residue 669 LEU Chi-restraints excluded: chain L residue 672 VAL Chi-restraints excluded: chain L residue 679 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 27 optimal weight: 3.9990 chunk 96 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 GLN E 696 GLN ** G 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 603 GLN ** H 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 610 GLN K 646 ASN L 603 GLN L 627 ASN ** L 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 677 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111994 restraints weight = 13914.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114597 restraints weight = 5797.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116083 restraints weight = 2982.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.116956 restraints weight = 1889.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.117417 restraints weight = 1414.539| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10200 Z= 0.162 Angle : 0.640 12.898 13704 Z= 0.302 Chirality : 0.031 0.148 1548 Planarity : 0.002 0.019 1896 Dihedral : 4.544 61.251 1356 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.59 % Allowed : 28.28 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 7.70 (0.17), residues: 1272 helix: 5.00 (0.10), residues: 1248 sheet: None (None), residues: 0 loop : -0.85 (0.92), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 666 PHE 0.015 0.001 PHE E 675 HIS 0.002 0.001 HIS G 698 Details of bonding type rmsd covalent geometry : bond 0.00345 (10200) covalent geometry : angle 0.64008 (13704) hydrogen bonds : bond 0.04869 ( 1198) hydrogen bonds : angle 3.38488 ( 3594) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 428 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 ASP cc_start: 0.8697 (t0) cc_final: 0.8097 (t0) REVERT: A 655 ASN cc_start: 0.9116 (t0) cc_final: 0.8844 (t0) REVERT: B 642 GLN cc_start: 0.8479 (mm110) cc_final: 0.8201 (tt0) REVERT: B 655 ASN cc_start: 0.9046 (t0) cc_final: 0.8590 (t0) REVERT: B 703 ASP cc_start: 0.8899 (m-30) cc_final: 0.8652 (m-30) REVERT: C 655 ASN cc_start: 0.8986 (t0) cc_final: 0.8430 (t0) REVERT: D 674 SER cc_start: 0.9190 (m) cc_final: 0.8764 (t) REVERT: D 688 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7902 (tm-30) REVERT: D 699 LYS cc_start: 0.8871 (tppt) cc_final: 0.8589 (tppt) REVERT: E 635 ASP cc_start: 0.8561 (t0) cc_final: 0.8079 (t0) REVERT: E 679 ARG cc_start: 0.7919 (tmm-80) cc_final: 0.7404 (tmm-80) REVERT: E 699 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8779 (tmtt) REVERT: F 702 MET cc_start: 0.9255 (tpp) cc_final: 0.8516 (tpp) REVERT: G 644 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8389 (pp30) REVERT: G 655 ASN cc_start: 0.9077 (t0) cc_final: 0.8801 (t0) REVERT: G 688 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7780 (tm-30) REVERT: H 635 ASP cc_start: 0.8703 (t70) cc_final: 0.8330 (t70) REVERT: H 644 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8085 (mm110) REVERT: H 655 ASN cc_start: 0.8763 (t0) cc_final: 0.8549 (t0) REVERT: H 666 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6673 (mpp80) REVERT: H 674 SER cc_start: 0.9045 (m) cc_final: 0.8656 (t) REVERT: H 709 GLN cc_start: 0.8290 (mm110) cc_final: 0.7141 (tm-30) REVERT: I 644 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8381 (pp30) REVERT: I 674 SER cc_start: 0.9012 (m) cc_final: 0.8719 (t) REVERT: I 699 LYS cc_start: 0.9056 (mmmt) cc_final: 0.8661 (mmmt) REVERT: I 709 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7372 (tm-30) REVERT: J 655 ASN cc_start: 0.8860 (t0) cc_final: 0.8409 (t0) REVERT: J 674 SER cc_start: 0.9116 (m) cc_final: 0.8760 (t) REVERT: J 681 GLU cc_start: 0.8519 (tp30) cc_final: 0.8116 (tp30) REVERT: K 676 GLN cc_start: 0.8343 (tt0) cc_final: 0.7546 (mt0) REVERT: K 679 ARG cc_start: 0.8077 (tmm-80) cc_final: 0.7822 (tmm-80) REVERT: L 642 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: L 674 SER cc_start: 0.8757 (m) cc_final: 0.8499 (t) REVERT: L 681 GLU cc_start: 0.8597 (mm-30) cc_final: 0.7993 (tm-30) outliers start: 49 outliers final: 37 residues processed: 440 average time/residue: 0.1135 time to fit residues: 65.3351 Evaluate side-chains 470 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 428 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain E residue 670 LYS Chi-restraints excluded: chain E residue 674 SER Chi-restraints excluded: chain E residue 699 LYS Chi-restraints excluded: chain F residue 622 LEU Chi-restraints excluded: chain F residue 632 LEU Chi-restraints excluded: chain F residue 658 ASP Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 710 SER Chi-restraints excluded: chain G residue 644 GLN Chi-restraints excluded: chain G residue 664 GLU Chi-restraints excluded: chain H residue 632 LEU Chi-restraints excluded: chain H residue 666 ARG Chi-restraints excluded: chain H residue 672 VAL Chi-restraints excluded: chain H residue 679 ARG Chi-restraints excluded: chain H residue 688 GLU Chi-restraints excluded: chain H residue 692 LYS Chi-restraints excluded: chain I residue 644 GLN Chi-restraints excluded: chain I residue 659 LEU Chi-restraints excluded: chain J residue 630 LEU Chi-restraints excluded: chain J residue 632 LEU Chi-restraints excluded: chain J residue 659 LEU Chi-restraints excluded: chain J residue 672 VAL Chi-restraints excluded: chain K residue 639 VAL Chi-restraints excluded: chain K residue 646 ASN Chi-restraints excluded: chain K residue 659 LEU Chi-restraints excluded: chain K residue 670 LYS Chi-restraints excluded: chain K residue 672 VAL Chi-restraints excluded: chain K residue 681 GLU Chi-restraints excluded: chain K residue 688 GLU Chi-restraints excluded: chain K residue 692 LYS Chi-restraints excluded: chain L residue 603 GLN Chi-restraints excluded: chain L residue 642 GLN Chi-restraints excluded: chain L residue 669 LEU Chi-restraints excluded: chain L residue 672 VAL Chi-restraints excluded: chain L residue 679 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 0.0070 chunk 103 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 GLN B 655 ASN ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 GLN E 696 GLN ** G 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 GLN J 610 GLN J 662 GLN K 646 ASN L 603 GLN L 627 ASN ** L 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.128060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.112950 restraints weight = 14152.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.115585 restraints weight = 5825.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117069 restraints weight = 2963.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.117966 restraints weight = 1867.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118446 restraints weight = 1390.064| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10200 Z= 0.152 Angle : 0.634 13.160 13704 Z= 0.297 Chirality : 0.030 0.197 1548 Planarity : 0.002 0.019 1896 Dihedral : 4.439 58.612 1356 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.49 % Allowed : 28.46 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 7.80 (0.17), residues: 1272 helix: 5.07 (0.10), residues: 1248 sheet: None (None), residues: 0 loop : -0.88 (0.95), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 666 PHE 0.013 0.001 PHE E 675 HIS 0.002 0.001 HIS G 698 Details of bonding type rmsd covalent geometry : bond 0.00317 (10200) covalent geometry : angle 0.63374 (13704) hydrogen bonds : bond 0.04843 ( 1198) hydrogen bonds : angle 3.32511 ( 3594) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1798.78 seconds wall clock time: 31 minutes 41.94 seconds (1901.94 seconds total)