Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 16:18:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0v_21985/07_2023/6x0v_21985_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0v_21985/07_2023/6x0v_21985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0v_21985/07_2023/6x0v_21985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0v_21985/07_2023/6x0v_21985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0v_21985/07_2023/6x0v_21985_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0v_21985/07_2023/6x0v_21985_neut.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 4 5.16 5 C 814 2.51 5 N 250 2.21 5 O 254 1.98 5 H 62 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 87": "NH1" <-> "NH2" Residue "H GLU 64": "OE1" <-> "OE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 1384 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 227 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 55 Chain: "F" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 475 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 324 Unresolved non-hydrogen angles: 414 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 169 Chain: "G" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 333 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 34} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 349 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Time building chain proxies: 1.30, per 1000 atoms: 0.94 Number of scatterers: 1384 At special positions: 0 Unit cell: (62.16, 60.088, 76.664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 254 8.00 N 250 7.00 C 814 6.00 H 62 1.00 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 - 3.50 Amino acid : False - 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: 0.74 Conformation dependent library (CDL) restraints added in 243.0 milliseconds 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 416 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 78.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'E' and resid 37 through 49 removed outlier: 3.610A pdb=" N ALA E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 65 removed outlier: 3.569A pdb=" N ASP E 61 " --> pdb=" O LYS E 57 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 79 Processing helix chain 'F' and resid 6 through 18 removed outlier: 3.576A pdb=" N LEU F 17 " --> pdb=" O LEU F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 46 through 56 removed outlier: 3.737A pdb=" N LYS F 50 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL F 51 " --> pdb=" O HIS F 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA F 54 " --> pdb=" O LYS F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 73 removed outlier: 4.347A pdb=" N TYR F 67 " --> pdb=" O PHE F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 87 Processing helix chain 'F' and resid 92 through 103 removed outlier: 3.747A pdb=" N TYR F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 90 removed outlier: 3.577A pdb=" N ASN G 65 " --> pdb=" O LYS G 61 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN G 76 " --> pdb=" O LYS G 72 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG G 80 " --> pdb=" O ASN G 76 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE G 81 " --> pdb=" O LEU G 77 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE G 83 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU G 84 " --> pdb=" O ARG G 80 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET G 88 " --> pdb=" O LEU G 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 91 removed outlier: 3.686A pdb=" N ASN H 65 " --> pdb=" O LYS H 61 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE H 67 " --> pdb=" O PHE H 63 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR H 68 " --> pdb=" O GLU H 64 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU H 77 " --> pdb=" O GLU H 73 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS H 78 " --> pdb=" O ASN H 74 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU H 86 " --> pdb=" O TYR H 82 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET H 88 " --> pdb=" O LEU H 84 " (cutoff:3.500A) 95 hydrogen bonds defined for protein. 285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.31 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 62 1.05 - 1.24: 103 1.24 - 1.43: 440 1.43 - 1.61: 775 1.61 - 1.80: 8 Bond restraints: 1388 Sorted by residual: bond pdb=" N ILE G 67 " pdb=" CA ILE G 67 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.76e+00 bond pdb=" N ILE G 67 " pdb=" H ILE G 67 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.51e+00 bond pdb=" N GLU G 69 " pdb=" H GLU G 69 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" N THR G 68 " pdb=" H THR G 68 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.46e+00 bond pdb=" N ASN G 65 " pdb=" H ASN G 65 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.44e+00 ... (remaining 1383 not shown) Histogram of bond angle deviations from ideal: 100.90 - 106.06: 9 106.06 - 111.22: 516 111.22 - 116.39: 352 116.39 - 121.55: 687 121.55 - 126.71: 361 Bond angle restraints: 1925 Sorted by residual: angle pdb=" C THR G 68 " pdb=" CA THR G 68 " pdb=" CB THR G 68 " ideal model delta sigma weight residual 110.85 117.31 -6.46 1.70e+00 3.46e-01 1.44e+01 angle pdb=" CA ILE H 67 " pdb=" C ILE H 67 " pdb=" O ILE H 67 " ideal model delta sigma weight residual 121.27 117.36 3.91 1.04e+00 9.25e-01 1.41e+01 angle pdb=" C THR G 68 " pdb=" N GLU G 69 " pdb=" CA GLU G 69 " ideal model delta sigma weight residual 120.28 125.28 -5.00 1.34e+00 5.57e-01 1.39e+01 angle pdb=" C GLU G 64 " pdb=" N ASN G 65 " pdb=" CA ASN G 65 " ideal model delta sigma weight residual 120.28 124.90 -4.62 1.34e+00 5.57e-01 1.19e+01 angle pdb=" C ASP G 62 " pdb=" N PHE G 63 " pdb=" CA PHE G 63 " ideal model delta sigma weight residual 120.28 124.80 -4.52 1.34e+00 5.57e-01 1.14e+01 ... (remaining 1920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.07: 709 10.07 - 20.15: 56 20.15 - 30.22: 31 30.22 - 40.29: 11 40.29 - 50.37: 3 Dihedral angle restraints: 810 sinusoidal: 186 harmonic: 624 Sorted by residual: dihedral pdb=" C THR G 68 " pdb=" N THR G 68 " pdb=" CA THR G 68 " pdb=" CB THR G 68 " ideal model delta harmonic sigma weight residual -122.00 -132.01 10.01 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" CA ARG F 18 " pdb=" C ARG F 18 " pdb=" N VAL F 19 " pdb=" CA VAL F 19 " ideal model delta harmonic sigma weight residual 180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLN G 66 " pdb=" CB GLN G 66 " pdb=" CG GLN G 66 " pdb=" CD GLN G 66 " ideal model delta sinusoidal sigma weight residual -60.00 -110.37 50.37 3 1.50e+01 4.44e-03 8.89e+00 ... (remaining 807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 178 0.049 - 0.098: 35 0.098 - 0.147: 7 0.147 - 0.196: 1 0.196 - 0.246: 1 Chirality restraints: 222 Sorted by residual: chirality pdb=" CA THR G 68 " pdb=" N THR G 68 " pdb=" C THR G 68 " pdb=" CB THR G 68 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ILE G 67 " pdb=" N ILE G 67 " pdb=" C ILE G 67 " pdb=" CB ILE G 67 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA ILE H 67 " pdb=" N ILE H 67 " pdb=" C ILE H 67 " pdb=" CB ILE H 67 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 219 not shown) Planarity restraints: 309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 61 " -0.025 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C LYS G 61 " 0.084 2.00e-02 2.50e+03 pdb=" O LYS G 61 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP G 62 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS G 61 " -0.013 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" N ASP G 62 " 0.042 2.00e-02 2.50e+03 pdb=" CA ASP G 62 " -0.011 2.00e-02 2.50e+03 pdb=" H ASP G 62 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 67 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C ILE H 67 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE H 67 " 0.010 2.00e-02 2.50e+03 pdb=" N THR H 68 " 0.009 2.00e-02 2.50e+03 ... (remaining 306 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 9 2.28 - 2.86: 830 2.86 - 3.44: 2029 3.44 - 4.02: 2255 4.02 - 4.60: 3249 Nonbonded interactions: 8372 Sorted by model distance: nonbonded pdb=" O ASN G 74 " pdb=" H LEU G 77 " model vdw 1.705 1.850 nonbonded pdb=" OE1 GLU H 64 " pdb=" H GLU H 64 " model vdw 1.733 1.850 nonbonded pdb=" O LYS H 71 " pdb=" H ASN H 74 " model vdw 1.775 1.850 nonbonded pdb=" O GLU H 86 " pdb=" H GLN H 89 " model vdw 1.817 1.850 nonbonded pdb=" O LYS G 78 " pdb=" H ILE G 81 " model vdw 1.939 1.850 ... (remaining 8367 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and resid 58 through 90) selection = (chain 'H' and (resid 58 through 89 or (resid 90 and (name N or name CA or name \ C or name O or name CB or name H )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 10.520 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.570 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 1326 Z= 0.211 Angle : 0.623 6.456 1801 Z= 0.469 Chirality : 0.043 0.246 222 Planarity : 0.003 0.049 247 Dihedral : 11.582 50.367 394 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.48 % Favored : 96.02 % Rotamer Outliers : 4.48 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.54), residues: 201 helix: -1.02 (0.42), residues: 145 sheet: None (None), residues: 0 loop : -2.95 (0.56), residues: 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Evaluate side-chains 20 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.212 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 20 average time/residue: 0.1716 time to fit residues: 3.9577 Evaluate side-chains 17 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.148 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0166 time to fit residues: 0.2219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.015 1326 Z= 0.132 Angle : 0.391 3.377 1801 Z= 0.233 Chirality : 0.035 0.127 222 Planarity : 0.002 0.011 247 Dihedral : 3.679 12.941 214 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.61), residues: 201 helix: 0.88 (0.44), residues: 159 sheet: None (None), residues: 0 loop : -3.00 (0.65), residues: 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Evaluate side-chains 24 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.175 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1246 time to fit residues: 3.5395 Evaluate side-chains 21 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.174 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 30.0000 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 30.0000 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.016 1326 Z= 0.143 Angle : 0.389 3.240 1801 Z= 0.230 Chirality : 0.036 0.131 222 Planarity : 0.002 0.008 247 Dihedral : 3.552 15.355 214 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.64), residues: 201 helix: 1.67 (0.45), residues: 159 sheet: None (None), residues: 0 loop : -2.75 (0.74), residues: 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Evaluate side-chains 22 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.182 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0937 time to fit residues: 2.5823 Evaluate side-chains 18 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 30.0000 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.023 1326 Z= 0.282 Angle : 0.592 6.388 1801 Z= 0.323 Chirality : 0.039 0.138 222 Planarity : 0.003 0.013 247 Dihedral : 4.565 21.437 214 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.62), residues: 201 helix: 1.12 (0.45), residues: 155 sheet: None (None), residues: 0 loop : -2.85 (0.73), residues: 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Evaluate side-chains 22 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.126 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0872 time to fit residues: 2.3109 Evaluate side-chains 18 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.123 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 40.0000 chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 0.0270 chunk 9 optimal weight: 30.0000 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.016 1326 Z= 0.132 Angle : 0.379 2.928 1801 Z= 0.225 Chirality : 0.036 0.131 222 Planarity : 0.002 0.006 247 Dihedral : 3.653 14.822 214 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.64), residues: 201 helix: 1.93 (0.45), residues: 156 sheet: None (None), residues: 0 loop : -2.81 (0.73), residues: 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Evaluate side-chains 22 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.169 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0977 time to fit residues: 2.6827 Evaluate side-chains 18 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.186 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 30.0000 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 5 optimal weight: 30.0000 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 30.0000 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.025 1326 Z= 0.301 Angle : 0.573 6.035 1801 Z= 0.317 Chirality : 0.039 0.139 222 Planarity : 0.003 0.013 247 Dihedral : 4.471 20.318 214 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.61), residues: 201 helix: 1.12 (0.44), residues: 156 sheet: None (None), residues: 0 loop : -2.88 (0.78), residues: 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Evaluate side-chains 23 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.207 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0922 time to fit residues: 2.6684 Evaluate side-chains 18 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.160 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 7 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 30.0000 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 0.0170 chunk 8 optimal weight: 0.9990 overall best weight: 0.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.019 1326 Z= 0.097 Angle : 0.322 2.617 1801 Z= 0.197 Chirality : 0.034 0.125 222 Planarity : 0.001 0.006 247 Dihedral : 3.326 13.655 214 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.64), residues: 201 helix: 2.42 (0.45), residues: 157 sheet: None (None), residues: 0 loop : -2.88 (0.74), residues: 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Evaluate side-chains 23 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.171 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0890 time to fit residues: 2.5773 Evaluate side-chains 19 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.174 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 13 optimal weight: 0.3980 chunk 2 optimal weight: 20.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.012 1326 Z= 0.088 Angle : 0.304 2.119 1801 Z= 0.187 Chirality : 0.035 0.129 222 Planarity : 0.001 0.007 247 Dihedral : 2.982 12.120 214 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.65), residues: 201 helix: 3.06 (0.45), residues: 155 sheet: None (None), residues: 0 loop : -3.14 (0.71), residues: 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Evaluate side-chains 23 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.172 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0971 time to fit residues: 2.8212 Evaluate side-chains 20 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.190 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 1 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 1326 Z= 0.220 Angle : 0.471 4.601 1801 Z= 0.270 Chirality : 0.038 0.134 222 Planarity : 0.002 0.011 247 Dihedral : 3.719 17.405 214 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.63), residues: 201 helix: 2.39 (0.44), residues: 157 sheet: None (None), residues: 0 loop : -2.73 (0.80), residues: 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Evaluate side-chains 21 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.176 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0903 time to fit residues: 2.4151 Evaluate side-chains 18 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.174 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 20.0000 chunk 7 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 1326 Z= 0.215 Angle : 0.461 4.382 1801 Z= 0.264 Chirality : 0.037 0.133 222 Planarity : 0.002 0.007 247 Dihedral : 3.895 17.987 214 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.63), residues: 201 helix: 2.14 (0.43), residues: 157 sheet: None (None), residues: 0 loop : -2.55 (0.90), residues: 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 61 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue ILE 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Evaluate side-chains 19 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.194 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0965 time to fit residues: 2.4199 Evaluate side-chains 18 residues out of total 197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.178 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 4 optimal weight: 20.0000 chunk 12 optimal weight: 40.0000 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.120361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118817 restraints weight = 4171.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.113236 restraints weight = 9315.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.112893 restraints weight = 9576.573| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.016 1326 Z= 0.150 Angle : 0.382 3.152 1801 Z= 0.225 Chirality : 0.036 0.131 222 Planarity : 0.002 0.007 247 Dihedral : 3.555 15.669 214 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.64), residues: 201 helix: 2.50 (0.44), residues: 158 sheet: None (None), residues: 0 loop : -2.51 (0.91), residues: 43 =============================================================================== Job complete usr+sys time: 709.15 seconds wall clock time: 14 minutes 19.97 seconds (859.97 seconds total)