Starting phenix.real_space_refine on Mon Dec 11 13:13:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lya_23590/12_2023/7lya_23590.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lya_23590/12_2023/7lya_23590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lya_23590/12_2023/7lya_23590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lya_23590/12_2023/7lya_23590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lya_23590/12_2023/7lya_23590.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lya_23590/12_2023/7lya_23590.pdb" } resolution = 2.91 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= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic. 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 293 5.49 5 S 14 5.16 5 C 6687 2.51 5 N 2275 2.21 5 O 2829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12098 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 737 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 735 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "C" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Time building chain proxies: 6.62, per 1000 atoms: 0.55 Number of scatterers: 12098 At special positions: 0 Unit cell: (86.604, 126.813, 117.534, 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 14 16.00 P 293 15.00 O 2829 8.00 N 2275 7.00 C 6687 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 - 3.50 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: 5.19 Conformation dependent library (CDL) restraints added in 1.4 seconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 71.4% alpha, 3.1% beta 139 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 6.04 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.539A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.606A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.548A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.719A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.550A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.595A pdb=" N MET D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.538A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.605A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.548A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.694A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.555A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.600A pdb=" N MET H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.607A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.520A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.507A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.732A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.697A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.695A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.127A 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 96 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.391A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.165A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.378A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 393 hydrogen bonds defined for protein. 1160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 4.46 Time building geometry restraints manager: 5.58 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: 2063 1.33 - 1.45: 4276 1.45 - 1.57: 5962 1.57 - 1.68: 584 1.68 - 1.80: 24 Bond restraints: 12909 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" CB ARG E 131 " pdb=" CG ARG E 131 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CB ARG A 131 " pdb=" CG ARG A 131 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CB ARG C 35 " pdb=" CG ARG C 35 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" CB LEU D 80 " pdb=" CG LEU D 80 " ideal model delta sigma weight residual 1.530 1.508 0.022 2.00e-02 2.50e+03 1.26e+00 ... (remaining 12904 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.04: 1266 105.04 - 111.92: 7038 111.92 - 118.80: 3279 118.80 - 125.68: 6124 125.68 - 132.56: 977 Bond angle restraints: 18684 Sorted by residual: angle pdb=" C GLN A 76 " pdb=" N ASP A 77 " pdb=" CA ASP A 77 " ideal model delta sigma weight residual 122.06 114.13 7.93 1.86e+00 2.89e-01 1.82e+01 angle pdb=" C GLN E 76 " pdb=" N ASP E 77 " pdb=" CA ASP E 77 " ideal model delta sigma weight residual 122.06 114.20 7.86 1.86e+00 2.89e-01 1.79e+01 angle pdb=" C LEU B 22 " pdb=" CA LEU B 22 " pdb=" CB LEU B 22 " ideal model delta sigma weight residual 110.96 115.76 -4.80 1.54e+00 4.22e-01 9.71e+00 angle pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N ARG B 23 " ideal model delta sigma weight residual 116.92 120.09 -3.17 1.16e+00 7.43e-01 7.48e+00 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 119.59 -6.41 2.37e+00 1.78e-01 7.33e+00 ... (remaining 18679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.23: 5575 34.23 - 68.45: 1429 68.45 - 102.68: 15 102.68 - 136.91: 0 136.91 - 171.14: 2 Dihedral angle restraints: 7021 sinusoidal: 4798 harmonic: 2223 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 48.86 171.14 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 71.26 148.74 1 3.50e+01 8.16e-04 1.45e+01 dihedral pdb=" CA LEU F 22 " pdb=" C LEU F 22 " pdb=" N ARG F 23 " pdb=" CA ARG F 23 " ideal model delta harmonic sigma weight residual -180.00 -161.07 -18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 7018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1134 0.029 - 0.058: 688 0.058 - 0.087: 220 0.087 - 0.116: 61 0.116 - 0.144: 21 Chirality restraints: 2124 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA ASP E 77 " pdb=" N ASP E 77 " pdb=" C ASP E 77 " pdb=" CB ASP E 77 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 2121 not shown) Planarity restraints: 1349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -52 " -0.007 2.00e-02 2.50e+03 1.17e-02 4.10e+00 pdb=" N9 DG I -52 " -0.001 2.00e-02 2.50e+03 pdb=" C8 DG I -52 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I -52 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I -52 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG I -52 " 0.012 2.00e-02 2.50e+03 pdb=" O6 DG I -52 " -0.014 2.00e-02 2.50e+03 pdb=" N1 DG I -52 " -0.008 2.00e-02 2.50e+03 pdb=" C2 DG I -52 " 0.030 2.00e-02 2.50e+03 pdb=" N2 DG I -52 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DG I -52 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I -52 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.026 2.00e-02 2.50e+03 1.09e-02 3.53e+00 pdb=" N9 DG I 47 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 57 " 0.024 2.00e-02 2.50e+03 1.05e-02 3.03e+00 pdb=" N9 DA I 57 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA I 57 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 57 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 57 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 57 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 57 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 57 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 57 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 57 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 57 " -0.004 2.00e-02 2.50e+03 ... (remaining 1346 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1674 2.76 - 3.47: 14035 3.47 - 4.19: 34080 4.19 - 4.90: 51718 Nonbonded interactions: 101509 Sorted by model distance: nonbonded pdb=" C SER D 123 " pdb=" N SER C 11 " model vdw 1.325 3.350 nonbonded pdb=" C SER H 123 " pdb=" N SER G 11 " model vdw 1.331 3.350 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.173 2.496 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.209 2.440 nonbonded pdb=" O SER D 123 " pdb=" N SER C 11 " model vdw 2.239 2.520 ... (remaining 101504 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 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = (chain 'C' and resid 11 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 123)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 4.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.320 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 37.590 Find NCS groups from input model: 0.460 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:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.007 0.046 12909 Z= 0.417 Angle : 0.671 7.927 18684 Z= 0.414 Chirality : 0.041 0.144 2124 Planarity : 0.004 0.040 1349 Dihedral : 27.352 171.135 5589 Min Nonbonded Distance : 1.325 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.16 % Allowed : 1.88 % Favored : 97.97 % 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: -1.91 (0.26), residues: 752 helix: -0.60 (0.20), residues: 537 sheet: None (None), residues: 0 loop : -2.78 (0.30), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 49 PHE 0.010 0.002 PHE E 84 TYR 0.012 0.002 TYR B 51 ARG 0.009 0.001 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.031 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 2.1559 time to fit residues: 244.4761 Evaluate side-chains 85 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 0.0980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN F 27 GLN F 75 HIS H 49 HIS C 73 ASN G 73 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12909 Z= 0.176 Angle : 0.546 6.894 18684 Z= 0.333 Chirality : 0.033 0.125 2124 Planarity : 0.004 0.037 1349 Dihedral : 29.735 173.485 4059 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.56 % Allowed : 9.06 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.72 (0.29), residues: 752 helix: 1.40 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -2.02 (0.33), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 75 PHE 0.008 0.001 PHE C 25 TYR 0.009 0.001 TYR D 121 ARG 0.004 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.901 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 94 average time/residue: 2.0362 time to fit residues: 201.4418 Evaluate side-chains 82 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.4151 time to fit residues: 3.9956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 HIS H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12909 Z= 0.237 Angle : 0.567 6.186 18684 Z= 0.343 Chirality : 0.035 0.130 2124 Planarity : 0.004 0.034 1349 Dihedral : 29.958 173.980 4059 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.56 % Allowed : 11.09 % Favored : 87.34 % 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: 1.46 (0.30), residues: 752 helix: 1.93 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.72 (0.34), 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 0.010 0.002 TYR D 121 ARG 0.003 0.000 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.994 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 89 average time/residue: 2.0062 time to fit residues: 188.2432 Evaluate side-chains 89 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 1.1875 time to fit residues: 6.1377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12909 Z= 0.244 Angle : 0.567 6.364 18684 Z= 0.342 Chirality : 0.035 0.149 2124 Planarity : 0.004 0.036 1349 Dihedral : 29.964 174.473 4059 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.19 % Allowed : 11.25 % Favored : 86.56 % 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: 1.66 (0.30), residues: 752 helix: 2.06 (0.23), residues: 543 sheet: None (None), residues: 0 loop : -1.58 (0.35), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.007 0.001 PHE F 61 TYR 0.010 0.001 TYR D 121 ARG 0.003 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.858 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 89 average time/residue: 2.0806 time to fit residues: 195.5420 Evaluate side-chains 90 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 1.2316 time to fit residues: 6.3578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12909 Z= 0.183 Angle : 0.559 6.945 18684 Z= 0.338 Chirality : 0.034 0.135 2124 Planarity : 0.004 0.036 1349 Dihedral : 29.959 174.427 4059 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.09 % Allowed : 13.12 % Favored : 85.78 % 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 (0.31), residues: 752 helix: 2.18 (0.23), residues: 543 sheet: None (None), residues: 0 loop : -1.49 (0.35), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.006 0.001 PHE B 61 TYR 0.009 0.001 TYR D 121 ARG 0.003 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.962 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 87 average time/residue: 2.0718 time to fit residues: 190.0421 Evaluate side-chains 89 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 1.5775 time to fit residues: 4.4363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 0.0970 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.0270 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12909 Z= 0.184 Angle : 0.553 6.657 18684 Z= 0.336 Chirality : 0.034 0.126 2124 Planarity : 0.004 0.036 1349 Dihedral : 29.948 174.570 4059 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.94 % Allowed : 13.28 % Favored : 85.78 % 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: 1.89 (0.31), residues: 752 helix: 2.22 (0.23), residues: 543 sheet: None (None), residues: 0 loop : -1.45 (0.35), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE B 61 TYR 0.009 0.001 TYR D 121 ARG 0.002 0.000 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.955 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 88 average time/residue: 2.0296 time to fit residues: 188.2616 Evaluate side-chains 88 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.0605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 81 optimal weight: 0.3980 chunk 96 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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: 0.8040 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12909 Z= 0.283 Angle : 0.586 7.195 18684 Z= 0.351 Chirality : 0.036 0.132 2124 Planarity : 0.004 0.038 1349 Dihedral : 30.093 175.411 4059 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.19 % Allowed : 11.88 % Favored : 85.94 % 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: 1.80 (0.30), residues: 752 helix: 2.13 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.40 (0.36), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.015 0.002 PHE A 78 TYR 0.010 0.002 TYR B 51 ARG 0.004 0.000 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.960 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 89 average time/residue: 2.0217 time to fit residues: 189.4811 Evaluate side-chains 88 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.8505 time to fit residues: 4.8691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12909 Z= 0.180 Angle : 0.565 7.388 18684 Z= 0.342 Chirality : 0.034 0.144 2124 Planarity : 0.004 0.037 1349 Dihedral : 30.069 175.278 4059 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.25 % Allowed : 13.12 % Favored : 85.62 % 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: 2.07 (0.31), residues: 752 helix: 2.32 (0.23), residues: 543 sheet: None (None), residues: 0 loop : -1.29 (0.36), 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 78 TYR 0.010 0.001 TYR B 51 ARG 0.003 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.880 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 84 average time/residue: 2.1176 time to fit residues: 187.2285 Evaluate side-chains 85 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.4136 time to fit residues: 2.4758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12909 Z= 0.256 Angle : 0.569 8.515 18684 Z= 0.341 Chirality : 0.035 0.133 2124 Planarity : 0.004 0.039 1349 Dihedral : 30.025 175.864 4059 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.41 % Allowed : 13.12 % Favored : 85.47 % 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: 2.06 (0.31), residues: 752 helix: 2.31 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.28 (0.36), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 49 PHE 0.011 0.001 PHE A 78 TYR 0.009 0.002 TYR D 121 ARG 0.003 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.882 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 84 average time/residue: 2.1109 time to fit residues: 186.6361 Evaluate side-chains 85 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 1.4952 time to fit residues: 4.2118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 99 optimal weight: 0.0570 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 1.0700 ------------------------------------------------------------------------------- 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: 0.8014 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12909 Z= 0.195 Angle : 0.561 7.990 18684 Z= 0.338 Chirality : 0.034 0.129 2124 Planarity : 0.004 0.039 1349 Dihedral : 30.019 175.819 4059 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.78 % Allowed : 13.91 % Favored : 85.31 % 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: 2.09 (0.30), residues: 752 helix: 2.33 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.27 (0.36), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.011 0.002 PHE A 78 TYR 0.009 0.001 TYR D 121 ARG 0.003 0.000 ARG H 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 1.045 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 83 average time/residue: 2.1531 time to fit residues: 187.8051 Evaluate side-chains 83 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.879 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.0462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.4345 > 50: distance: 93 - 114: 8.062 distance: 97 - 125: 4.394 distance: 105 - 114: 9.277 distance: 114 - 115: 5.954 distance: 115 - 116: 24.633 distance: 115 - 118: 6.194 distance: 116 - 117: 20.601 distance: 116 - 125: 20.286 distance: 118 - 119: 10.341 distance: 119 - 120: 5.047 distance: 120 - 121: 6.540 distance: 122 - 123: 3.369 distance: 122 - 124: 3.401 distance: 125 - 126: 22.434 distance: 126 - 127: 15.816 distance: 127 - 128: 16.821 distance: 127 - 129: 14.315 distance: 129 - 130: 12.194 distance: 130 - 131: 5.481 distance: 131 - 132: 25.152 distance: 131 - 133: 25.723 distance: 133 - 134: 17.666 distance: 134 - 135: 7.158 distance: 134 - 137: 22.579 distance: 135 - 136: 16.302 distance: 135 - 140: 6.221 distance: 137 - 138: 19.218 distance: 137 - 139: 24.031 distance: 140 - 141: 5.331 distance: 141 - 142: 6.385 distance: 141 - 144: 4.501 distance: 142 - 143: 19.872 distance: 142 - 149: 5.716 distance: 144 - 145: 4.094 distance: 145 - 146: 3.278 distance: 146 - 147: 5.337 distance: 149 - 150: 4.790 distance: 150 - 151: 4.688 distance: 151 - 152: 5.924 distance: 151 - 160: 4.779 distance: 153 - 154: 4.784 distance: 154 - 155: 4.096 distance: 160 - 161: 7.294 distance: 161 - 162: 10.008 distance: 162 - 163: 18.045 distance: 162 - 168: 11.808 distance: 164 - 166: 5.840 distance: 168 - 169: 10.771 distance: 169 - 170: 11.304 distance: 169 - 172: 18.075 distance: 170 - 171: 21.860 distance: 170 - 174: 6.655 distance: 172 - 173: 12.901 distance: 174 - 175: 20.879 distance: 175 - 176: 11.757 distance: 176 - 177: 7.610 distance: 176 - 178: 7.101 distance: 178 - 179: 8.297 distance: 179 - 180: 6.794 distance: 179 - 182: 3.154 distance: 180 - 181: 14.929 distance: 180 - 186: 6.572 distance: 182 - 183: 4.636 distance: 183 - 184: 7.699 distance: 183 - 185: 7.761