Starting phenix.real_space_refine on Mon Dec 30 01:13:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qzm_18778/12_2024/8qzm_18778.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qzm_18778/12_2024/8qzm_18778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qzm_18778/12_2024/8qzm_18778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qzm_18778/12_2024/8qzm_18778.map" model { file = "/net/cci-nas-00/data/ceres_data/8qzm_18778/12_2024/8qzm_18778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qzm_18778/12_2024/8qzm_18778.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 11 5.16 5 C 6718 2.51 5 N 2292 2.21 5 O 2830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12141 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 189 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 7.59, per 1000 atoms: 0.63 Number of scatterers: 12141 At special positions: 0 Unit cell: (77.926, 121.863, 117.718, 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 11 16.00 P 290 15.00 O 2830 8.00 N 2292 7.00 C 6718 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: 3.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1462 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 69.7% alpha, 2.8% beta 137 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 6.10 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.680A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.610A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.554A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.560A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.842A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.586A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.787A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.671A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.969A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.499A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.643A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.216A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.396A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 406 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 355 hydrogen bonds 710 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2357 1.33 - 1.45: 4234 1.45 - 1.57: 5753 1.57 - 1.69: 578 1.69 - 1.81: 22 Bond restraints: 12944 Sorted by residual: bond pdb=" P DG I 20 " pdb=" OP2 DG I 20 " ideal model delta sigma weight residual 1.480 1.520 -0.040 2.00e-02 2.50e+03 4.03e+00 bond pdb=" P DT I -59 " pdb=" OP2 DT I -59 " ideal model delta sigma weight residual 1.480 1.520 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" P DC I 52 " pdb=" OP2 DC I 52 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb=" P DG I 21 " pdb=" OP1 DG I 21 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" P DC I 53 " pdb=" OP1 DC I 53 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.64e+00 ... (remaining 12939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 18376 1.93 - 3.85: 309 3.85 - 5.78: 16 5.78 - 7.71: 14 7.71 - 9.64: 2 Bond angle restraints: 18717 Sorted by residual: angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 111.02 116.92 -5.90 1.86e+00 2.89e-01 1.00e+01 angle pdb=" CA LEU D 101 " pdb=" CB LEU D 101 " pdb=" CG LEU D 101 " ideal model delta sigma weight residual 116.30 125.94 -9.64 3.50e+00 8.16e-02 7.58e+00 angle pdb=" C3' DC I 53 " pdb=" C2' DC I 53 " pdb=" C1' DC I 53 " ideal model delta sigma weight residual 101.60 105.63 -4.03 1.50e+00 4.44e-01 7.20e+00 angle pdb=" CB MET A 90 " pdb=" CG MET A 90 " pdb=" SD MET A 90 " ideal model delta sigma weight residual 112.70 120.68 -7.98 3.00e+00 1.11e-01 7.08e+00 angle pdb=" C4 DT I -59 " pdb=" C5 DT I -59 " pdb=" C7 DT I -59 " ideal model delta sigma weight residual 122.40 118.56 3.84 1.50e+00 4.44e-01 6.56e+00 ... (remaining 18712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.29: 5477 32.29 - 64.58: 1525 64.58 - 96.87: 40 96.87 - 129.16: 0 129.16 - 161.45: 3 Dihedral angle restraints: 7045 sinusoidal: 4780 harmonic: 2265 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 58.55 161.45 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 66.42 153.58 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 69.26 150.74 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 7042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 2113 0.120 - 0.239: 8 0.239 - 0.359: 1 0.359 - 0.478: 0 0.478 - 0.598: 6 Chirality restraints: 2128 Sorted by residual: chirality pdb=" P DC I -58 " pdb=" OP1 DC I -58 " pdb=" OP2 DC I -58 " pdb=" O5' DC I -58 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.94e+00 chirality pdb=" P DG I 21 " pdb=" OP1 DG I 21 " pdb=" OP2 DG I 21 " pdb=" O5' DG I 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.92 -0.58 2.00e-01 2.50e+01 8.34e+00 chirality pdb=" P DC I 53 " pdb=" OP1 DC I 53 " pdb=" OP2 DC I 53 " pdb=" O5' DC I 53 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.55 2.00e-01 2.50e+01 7.52e+00 ... (remaining 2125 not shown) Planarity restraints: 1366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.56e+00 pdb=" N PRO H 103 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -55 " -0.023 2.00e-02 2.50e+03 9.99e-03 2.74e+00 pdb=" N9 DA I -55 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DA I -55 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I -55 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I -55 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -55 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I -55 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -55 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I -55 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I -55 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -55 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 57 " 0.023 2.00e-02 2.50e+03 9.44e-03 2.67e+00 pdb=" N9 DG I 57 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DG I 57 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 57 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 57 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 57 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 57 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 57 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 57 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 57 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 57 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 57 " -0.001 2.00e-02 2.50e+03 ... (remaining 1363 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2319 2.79 - 3.31: 10898 3.31 - 3.84: 23587 3.84 - 4.37: 28097 4.37 - 4.90: 40245 Nonbonded interactions: 105146 Sorted by model distance: nonbonded pdb=" OE2 GLU G 61 " pdb=" NH1 ARG K 181 " model vdw 2.257 3.120 nonbonded pdb=" NE2 GLN E 125 " pdb=" OE2 GLU F 53 " model vdw 2.265 3.120 nonbonded pdb=" OG1 THR F 30 " pdb=" OP2 DC J -12 " model vdw 2.306 3.040 nonbonded pdb=" O LEU A 92 " pdb=" OG SER A 96 " model vdw 2.314 3.040 nonbonded pdb=" NH2 ARG F 35 " pdb=" OP2 DG I 8 " model vdw 2.315 3.120 ... (remaining 105141 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' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 10 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = chain '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 individual isotropic 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.570 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 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 : 0.004 0.040 12944 Z= 0.247 Angle : 0.600 9.637 18717 Z= 0.350 Chirality : 0.046 0.598 2128 Planarity : 0.004 0.047 1366 Dihedral : 28.215 161.446 5583 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.31 % Allowed : 11.04 % Favored : 88.65 % 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: 1.83 (0.30), residues: 763 helix: 1.82 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.22 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.008 0.001 PHE H 70 TYR 0.015 0.001 TYR A 41 ARG 0.005 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 108 LYS cc_start: 0.8726 (ttpt) cc_final: 0.8392 (ttmt) outliers start: 2 outliers final: 1 residues processed: 136 average time/residue: 0.4196 time to fit residues: 72.3955 Evaluate side-chains 118 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 90 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12944 Z= 0.228 Angle : 0.551 8.288 18717 Z= 0.330 Chirality : 0.034 0.159 2128 Planarity : 0.004 0.043 1366 Dihedral : 30.405 163.858 4044 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.40 % Allowed : 11.66 % Favored : 86.94 % 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: 2.34 (0.30), residues: 763 helix: 2.21 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.22 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE A 67 TYR 0.012 0.001 TYR H 40 ARG 0.003 0.000 ARG K 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7509 (tp30) cc_final: 0.7264 (tp30) REVERT: E 49 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8306 (ptp-170) REVERT: K 187 ARG cc_start: 0.8306 (tpt-90) cc_final: 0.7878 (tpt-90) outliers start: 9 outliers final: 5 residues processed: 139 average time/residue: 0.3716 time to fit residues: 66.4546 Evaluate side-chains 127 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN G 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12944 Z= 0.283 Angle : 0.559 5.683 18717 Z= 0.336 Chirality : 0.035 0.148 2128 Planarity : 0.004 0.041 1366 Dihedral : 30.446 165.419 4041 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.71 % Allowed : 13.22 % Favored : 85.07 % 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: 2.41 (0.30), residues: 763 helix: 2.30 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.34 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE A 67 TYR 0.011 0.001 TYR A 41 ARG 0.004 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7901 (tm-30) REVERT: D 93 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8316 (mp0) REVERT: E 49 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8292 (ptp-170) outliers start: 11 outliers final: 8 residues processed: 137 average time/residue: 0.3720 time to fit residues: 65.6171 Evaluate side-chains 130 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 125 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12944 Z= 0.334 Angle : 0.579 5.391 18717 Z= 0.346 Chirality : 0.036 0.153 2128 Planarity : 0.004 0.039 1366 Dihedral : 30.583 165.517 4041 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.18 % Allowed : 14.15 % Favored : 83.67 % 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: 2.36 (0.30), residues: 763 helix: 2.31 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.47 (0.38), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 49 PHE 0.011 0.001 PHE A 67 TYR 0.012 0.001 TYR A 41 ARG 0.005 0.000 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7813 (tm-30) REVERT: D 93 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8350 (mp0) REVERT: E 49 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8457 (ptp-170) REVERT: E 125 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8405 (mm-40) outliers start: 14 outliers final: 9 residues processed: 135 average time/residue: 0.3699 time to fit residues: 64.5865 Evaluate side-chains 131 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 125 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12944 Z= 0.329 Angle : 0.579 5.383 18717 Z= 0.346 Chirality : 0.036 0.152 2128 Planarity : 0.004 0.036 1366 Dihedral : 30.640 165.327 4041 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.33 % Allowed : 15.40 % Favored : 82.27 % 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: 2.37 (0.30), residues: 763 helix: 2.32 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.47 (0.38), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 49 PHE 0.010 0.001 PHE A 67 TYR 0.012 0.001 TYR A 41 ARG 0.004 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: C 41 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7751 (tm-30) REVERT: D 93 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: E 49 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8287 (ptp-170) REVERT: K 187 ARG cc_start: 0.8489 (tpt-90) cc_final: 0.7953 (tpt-90) outliers start: 15 outliers final: 9 residues processed: 135 average time/residue: 0.4010 time to fit residues: 69.6056 Evaluate side-chains 129 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12944 Z= 0.371 Angle : 0.599 5.772 18717 Z= 0.357 Chirality : 0.037 0.159 2128 Planarity : 0.004 0.039 1366 Dihedral : 30.815 164.987 4041 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.33 % Allowed : 16.02 % Favored : 81.65 % 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: 2.32 (0.30), residues: 763 helix: 2.28 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.50 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 49 PHE 0.010 0.001 PHE A 67 TYR 0.013 0.001 TYR A 41 ARG 0.004 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: C 41 GLU cc_start: 0.8282 (tm-30) cc_final: 0.8033 (tm-30) REVERT: K 187 ARG cc_start: 0.8528 (tpt-90) cc_final: 0.7985 (tpt-90) outliers start: 15 outliers final: 10 residues processed: 133 average time/residue: 0.4026 time to fit residues: 69.4734 Evaluate side-chains 126 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12944 Z= 0.209 Angle : 0.548 6.917 18717 Z= 0.330 Chirality : 0.033 0.153 2128 Planarity : 0.003 0.036 1366 Dihedral : 30.318 163.808 4041 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.56 % Allowed : 16.64 % Favored : 81.80 % 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: 2.64 (0.30), residues: 763 helix: 2.48 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.30 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE A 67 TYR 0.012 0.001 TYR H 40 ARG 0.004 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.933 Fit side-chains REVERT: C 41 GLU cc_start: 0.8280 (tm-30) cc_final: 0.8017 (tm-30) REVERT: K 187 ARG cc_start: 0.8482 (tpt-90) cc_final: 0.7978 (tpt-90) outliers start: 10 outliers final: 7 residues processed: 142 average time/residue: 0.3613 time to fit residues: 66.5267 Evaluate side-chains 126 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 12944 Z= 0.397 Angle : 0.622 10.705 18717 Z= 0.366 Chirality : 0.038 0.158 2128 Planarity : 0.004 0.036 1366 Dihedral : 30.798 164.083 4041 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.18 % Allowed : 16.80 % Favored : 81.03 % 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: 2.30 (0.30), residues: 763 helix: 2.27 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.49 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.011 0.001 PHE H 70 TYR 0.015 0.001 TYR A 54 ARG 0.005 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.994 Fit side-chains REVERT: C 41 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8031 (tm-30) REVERT: K 187 ARG cc_start: 0.8534 (tpt-90) cc_final: 0.7992 (tpt-90) outliers start: 14 outliers final: 11 residues processed: 131 average time/residue: 0.3712 time to fit residues: 63.2082 Evaluate side-chains 126 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12944 Z= 0.271 Angle : 0.578 10.271 18717 Z= 0.344 Chirality : 0.034 0.155 2128 Planarity : 0.004 0.036 1366 Dihedral : 30.579 163.518 4041 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.56 % Allowed : 17.11 % Favored : 81.34 % 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: 2.48 (0.30), residues: 763 helix: 2.37 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.38 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE H 70 TYR 0.013 0.001 TYR H 83 ARG 0.004 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.980 Fit side-chains REVERT: C 41 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8018 (tm-30) REVERT: K 187 ARG cc_start: 0.8475 (tpt-90) cc_final: 0.7978 (tpt-90) outliers start: 10 outliers final: 10 residues processed: 125 average time/residue: 0.3713 time to fit residues: 60.0824 Evaluate side-chains 123 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12944 Z= 0.202 Angle : 0.561 12.176 18717 Z= 0.333 Chirality : 0.033 0.154 2128 Planarity : 0.003 0.036 1366 Dihedral : 30.196 162.593 4041 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.40 % Allowed : 17.57 % Favored : 81.03 % 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: 2.71 (0.30), residues: 763 helix: 2.51 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.19 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE H 70 TYR 0.012 0.001 TYR H 40 ARG 0.004 0.000 ARG F 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.926 Fit side-chains REVERT: C 41 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7984 (tm-30) REVERT: K 187 ARG cc_start: 0.8450 (tpt-90) cc_final: 0.7966 (tpt-90) outliers start: 9 outliers final: 9 residues processed: 138 average time/residue: 0.3428 time to fit residues: 62.4207 Evaluate side-chains 127 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.057144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.042998 restraints weight = 47008.133| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.82 r_work: 0.2726 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12944 Z= 0.207 Angle : 0.568 11.532 18717 Z= 0.335 Chirality : 0.033 0.153 2128 Planarity : 0.003 0.037 1366 Dihedral : 30.203 162.247 4041 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.71 % Allowed : 17.73 % Favored : 80.56 % 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: 2.77 (0.30), residues: 763 helix: 2.54 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.10 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE A 67 TYR 0.011 0.001 TYR F 88 ARG 0.004 0.000 ARG H 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2291.57 seconds wall clock time: 42 minutes 51.97 seconds (2571.97 seconds total)