Starting phenix.real_space_refine on Sat Dec 9 09:18:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv8_23529/12_2023/7lv8_23529.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv8_23529/12_2023/7lv8_23529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv8_23529/12_2023/7lv8_23529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv8_23529/12_2023/7lv8_23529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv8_23529/12_2023/7lv8_23529.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lv8_23529/12_2023/7lv8_23529.pdb" } resolution = 3.4 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= 1.001 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 242 5.49 5 S 30 5.16 5 C 5913 2.51 5 N 1961 2.21 5 O 2505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 18": "OD1" <-> "OD2" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "F ASP 18": "OD1" <-> "OD2" Residue "F ASP 102": "OD1" <-> "OD2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G GLU 155": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10651 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 731 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "A" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 770 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 659 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 688 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 731 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "E" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 772 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 659 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 680 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 93} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2495 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Chain: "J" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2466 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Time building chain proxies: 5.69, per 1000 atoms: 0.53 Number of scatterers: 10651 At special positions: 0 Unit cell: (82.84, 115.54, 118.81, 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 30 16.00 P 242 15.00 O 2505 8.00 N 1961 7.00 C 5913 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: 5.20 Conformation dependent library (CDL) restraints added in 987.7 milliseconds 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 7 sheets defined 67.8% alpha, 1.8% beta 112 base pairs and 205 stacking pairs defined. Time for finding SS restraints: 4.67 Creating SS restraints... Processing helix chain 'B' and resid 28 through 39 removed outlier: 3.660A pdb=" N LEU B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 74 removed outlier: 3.675A pdb=" N LEU B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 removed outlier: 3.554A pdb=" N VAL B 84 " --> pdb=" O MET B 80 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 136 removed outlier: 3.511A pdb=" N VAL A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.739A pdb=" N LYS A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 195 removed outlier: 3.503A pdb=" N ILE A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 211 removed outlier: 3.603A pdb=" N ILE A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 35 through 61 Processing helix chain 'D' and resid 69 through 81 removed outlier: 3.753A pdb=" N VAL D 73 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 103 removed outlier: 3.745A pdb=" N GLY D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 92 " --> pdb=" O HIS D 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 138 through 167 removed outlier: 3.561A pdb=" N ALA C 142 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 184 removed outlier: 3.592A pdb=" N ASP C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 192 removed outlier: 3.538A pdb=" N ALA C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL C 190 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 40 removed outlier: 3.570A pdb=" N GLN F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA F 39 " --> pdb=" O LEU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 74 removed outlier: 3.595A pdb=" N LEU F 69 " --> pdb=" O GLN F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 89 removed outlier: 3.545A pdb=" N VAL F 84 " --> pdb=" O MET F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 92 No H-bonds generated for 'chain 'F' and resid 90 through 92' Processing helix chain 'E' and resid 127 through 136 removed outlier: 3.525A pdb=" N VAL E 132 " --> pdb=" O ASN E 128 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET E 136 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 160 removed outlier: 3.848A pdb=" N GLU E 159 " --> pdb=" O ILE E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 195 removed outlier: 3.586A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 211 removed outlier: 3.717A pdb=" N ILE E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 29 Processing helix chain 'H' and resid 35 through 61 Processing helix chain 'H' and resid 69 through 81 removed outlier: 3.698A pdb=" N VAL H 73 " --> pdb=" O LYS H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 103 removed outlier: 3.547A pdb=" N GLY H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 120 through 130 Processing helix chain 'G' and resid 138 through 167 removed outlier: 3.771A pdb=" N ALA G 142 " --> pdb=" O SER G 138 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE G 152 " --> pdb=" O ALA G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 183 removed outlier: 3.545A pdb=" N ILE G 181 " --> pdb=" O ILE G 177 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN G 182 " --> pdb=" O THR G 178 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN G 183 " --> pdb=" O LEU G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 189 removed outlier: 3.735A pdb=" N ALA G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 78 through 79 Processing sheet with id=AA2, first strand: chain 'D' and resid 33 through 34 removed outlier: 7.315A pdb=" N SER D 33 " --> pdb=" O ILE C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 67 through 68 Processing sheet with id=AA4, first strand: chain 'F' and resid 43 through 44 removed outlier: 6.959A pdb=" N SER F 43 " --> pdb=" O VAL E 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'H' and resid 33 through 34 removed outlier: 7.202A pdb=" N SER H 33 " --> pdb=" O ILE G 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 67 through 68 350 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 291 hydrogen bonds 578 hydrogen bond angles 0 basepair planarities 112 basepair parallelities 205 stacking parallelities Total time for adding SS restraints: 3.88 Time building geometry restraints manager: 5.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2538 1.34 - 1.46: 3383 1.46 - 1.58: 4857 1.58 - 1.70: 482 1.70 - 1.82: 52 Bond restraints: 11312 Sorted by residual: bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.34e+00 bond pdb=" CB ASP F 47 " pdb=" CG ASP F 47 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.33e+00 bond pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.78e+00 bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.26e+00 bond pdb=" CB ASN D 16 " pdb=" CG ASN D 16 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.81e+00 ... (remaining 11307 not shown) Histogram of bond angle deviations from ideal: 97.74 - 104.72: 954 104.72 - 111.69: 6037 111.69 - 118.67: 3172 118.67 - 125.65: 5307 125.65 - 132.62: 819 Bond angle restraints: 16289 Sorted by residual: angle pdb=" CB MET C 153 " pdb=" CG MET C 153 " pdb=" SD MET C 153 " ideal model delta sigma weight residual 112.70 124.35 -11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C LYS C 107 " pdb=" N GLU C 108 " pdb=" CA GLU C 108 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 124.92 -4.72 1.50e+00 4.44e-01 9.89e+00 angle pdb=" CA LYS C 107 " pdb=" CB LYS C 107 " pdb=" CG LYS C 107 " ideal model delta sigma weight residual 114.10 120.11 -6.01 2.00e+00 2.50e-01 9.02e+00 angle pdb=" CB ASP F 47 " pdb=" CG ASP F 47 " pdb=" OD1 ASP F 47 " ideal model delta sigma weight residual 118.40 124.93 -6.53 2.30e+00 1.89e-01 8.05e+00 ... (remaining 16284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.62: 5028 34.62 - 69.24: 1127 69.24 - 103.86: 18 103.86 - 138.48: 0 138.48 - 173.11: 3 Dihedral angle restraints: 6176 sinusoidal: 4008 harmonic: 2168 Sorted by residual: 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 46.89 173.11 1 3.50e+01 8.16e-04 1.56e+01 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 76.29 143.71 1 3.50e+01 8.16e-04 1.42e+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 80.70 139.30 1 3.50e+01 8.16e-04 1.38e+01 ... (remaining 6173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1332 0.033 - 0.066: 410 0.066 - 0.098: 106 0.098 - 0.131: 37 0.131 - 0.164: 6 Chirality restraints: 1891 Sorted by residual: 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 -2.51 -0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA ILE F 27 " pdb=" N ILE F 27 " pdb=" C ILE F 27 " pdb=" CB ILE F 27 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA ASN D 16 " pdb=" N ASN D 16 " pdb=" C ASN D 16 " pdb=" CB ASN D 16 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 1888 not shown) Planarity restraints: 1211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 47 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C ASP F 47 " 0.055 2.00e-02 2.50e+03 pdb=" O ASP F 47 " -0.021 2.00e-02 2.50e+03 pdb=" N THR F 48 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 178 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" CD GLU A 178 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU A 178 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 178 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 36 " 0.023 2.00e-02 2.50e+03 1.13e-02 2.88e+00 pdb=" N1 DC J 36 " -0.017 2.00e-02 2.50e+03 pdb=" C2 DC J 36 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DC J 36 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC J 36 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC J 36 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC J 36 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DC J 36 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DC J 36 " -0.005 2.00e-02 2.50e+03 ... (remaining 1208 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.05: 4 2.05 - 2.76: 1484 2.76 - 3.47: 13337 3.47 - 4.19: 29814 4.19 - 4.90: 43158 Nonbonded interactions: 87797 Sorted by model distance: nonbonded pdb=" C LYS H 104 " pdb=" N GLU G 105 " model vdw 1.334 3.350 nonbonded pdb=" C SER F 112 " pdb=" N CYS E 113 " model vdw 1.335 3.350 nonbonded pdb=" C SER B 112 " pdb=" N CYS A 113 " model vdw 1.337 3.350 nonbonded pdb=" C LYS D 104 " pdb=" N GLU C 105 " model vdw 1.337 3.350 nonbonded pdb=" O LYS B 29 " pdb=" OG1 THR B 32 " model vdw 2.205 2.440 ... (remaining 87792 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' and (resid 113 through 122 or (resid 123 and (name N or name CA or na \ me C or name O or name CB )) or resid 124 through 214)) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 105 through 106 or (resid 107 through 108 and (name N or n \ ame CA or name C or name O or name CB )) or resid 109 through 157 or (resid 158 \ and (name N or name CA or name C or name O or name CB )) or resid 159 through 19 \ 8)) selection = chain 'G' } 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: 1.190 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: 4.210 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 34.450 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11312 Z= 0.188 Angle : 0.646 11.653 16289 Z= 0.388 Chirality : 0.037 0.164 1891 Planarity : 0.004 0.046 1211 Dihedral : 27.117 173.105 4772 Min Nonbonded Distance : 1.334 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.17 % Allowed : 0.00 % Favored : 99.83 % 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: -3.26 (0.22), residues: 748 helix: -2.34 (0.15), residues: 488 sheet: None (None), residues: 0 loop : -1.37 (0.32), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 57 PHE 0.024 0.002 PHE G 152 TYR 0.024 0.003 TYR H 100 ARG 0.012 0.001 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.867 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 110 average time/residue: 0.2586 time to fit residues: 39.0809 Evaluate side-chains 68 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1080 time to fit residues: 1.2315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.0670 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 128 ASN G 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11312 Z= 0.196 Angle : 0.556 8.174 16289 Z= 0.335 Chirality : 0.033 0.149 1891 Planarity : 0.004 0.037 1211 Dihedral : 29.602 169.532 3430 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.34 % Allowed : 8.68 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.19 (0.28), residues: 748 helix: 0.86 (0.22), residues: 498 sheet: None (None), residues: 0 loop : -1.32 (0.33), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 57 PHE 0.030 0.002 PHE G 152 TYR 0.014 0.001 TYR D 81 ARG 0.006 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.859 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 87 average time/residue: 0.2341 time to fit residues: 29.0555 Evaluate side-chains 72 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1019 time to fit residues: 2.1387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 59 optimal weight: 0.0770 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 ASN D 35 GLN G 176 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 11312 Z= 0.420 Angle : 0.695 8.289 16289 Z= 0.398 Chirality : 0.041 0.181 1891 Planarity : 0.004 0.042 1211 Dihedral : 29.920 170.311 3430 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.50 % Allowed : 11.02 % Favored : 86.48 % 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: 0.77 (0.30), residues: 748 helix: 1.39 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -1.27 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 34 PHE 0.045 0.004 PHE G 152 TYR 0.036 0.003 TYR H 81 ARG 0.008 0.001 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.874 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 86 average time/residue: 0.2147 time to fit residues: 27.2790 Evaluate side-chains 79 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1046 time to fit residues: 2.7345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 41 optimal weight: 0.0060 chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11312 Z= 0.265 Angle : 0.577 6.748 16289 Z= 0.342 Chirality : 0.035 0.143 1891 Planarity : 0.003 0.034 1211 Dihedral : 29.743 171.384 3430 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.67 % Allowed : 11.69 % Favored : 86.64 % 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: 1.57 (0.31), residues: 748 helix: 2.06 (0.23), residues: 494 sheet: None (None), residues: 0 loop : -1.06 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 55 PHE 0.035 0.002 PHE G 152 TYR 0.026 0.002 TYR H 81 ARG 0.006 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.920 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 82 average time/residue: 0.2269 time to fit residues: 28.0490 Evaluate side-chains 76 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1110 time to fit residues: 2.3867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11312 Z= 0.274 Angle : 0.592 6.303 16289 Z= 0.349 Chirality : 0.036 0.145 1891 Planarity : 0.003 0.033 1211 Dihedral : 29.789 170.812 3430 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.84 % Allowed : 15.19 % Favored : 82.97 % 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: 1.77 (0.31), residues: 748 helix: 2.23 (0.23), residues: 494 sheet: None (None), residues: 0 loop : -1.02 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 55 PHE 0.039 0.003 PHE G 152 TYR 0.025 0.002 TYR H 81 ARG 0.004 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.914 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 80 average time/residue: 0.2123 time to fit residues: 25.0623 Evaluate side-chains 73 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0975 time to fit residues: 1.8060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 ASN H 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11312 Z= 0.256 Angle : 0.573 5.849 16289 Z= 0.340 Chirality : 0.035 0.136 1891 Planarity : 0.003 0.027 1211 Dihedral : 29.731 171.042 3430 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.34 % Allowed : 15.69 % Favored : 81.97 % 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: 1.97 (0.31), residues: 748 helix: 2.38 (0.23), residues: 494 sheet: None (None), residues: 0 loop : -0.94 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 55 PHE 0.035 0.003 PHE C 152 TYR 0.020 0.002 TYR H 81 ARG 0.003 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.821 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 85 average time/residue: 0.2078 time to fit residues: 26.2421 Evaluate side-chains 80 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.775 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0998 time to fit residues: 2.6222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.7713 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11312 Z= 0.217 Angle : 0.551 6.367 16289 Z= 0.329 Chirality : 0.034 0.130 1891 Planarity : 0.003 0.028 1211 Dihedral : 29.660 170.398 3430 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.67 % Allowed : 17.70 % Favored : 81.64 % 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: 2.16 (0.31), residues: 748 helix: 2.52 (0.23), residues: 494 sheet: None (None), residues: 0 loop : -0.85 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 55 PHE 0.033 0.002 PHE G 152 TYR 0.011 0.002 TYR H 81 ARG 0.003 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 1.034 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 85 average time/residue: 0.2507 time to fit residues: 31.2903 Evaluate side-chains 77 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0958 time to fit residues: 1.5641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 11312 Z= 0.495 Angle : 0.744 8.548 16289 Z= 0.421 Chirality : 0.043 0.183 1891 Planarity : 0.004 0.044 1211 Dihedral : 30.225 171.724 3430 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.50 % Allowed : 17.70 % Favored : 80.80 % 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: 1.32 (0.30), residues: 748 helix: 1.85 (0.23), residues: 492 sheet: None (None), residues: 0 loop : -1.09 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 34 PHE 0.057 0.004 PHE C 152 TYR 0.017 0.002 TYR D 81 ARG 0.006 0.001 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 1.044 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 81 average time/residue: 0.2420 time to fit residues: 28.0178 Evaluate side-chains 78 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0974 time to fit residues: 2.3342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11312 Z= 0.225 Angle : 0.573 7.181 16289 Z= 0.338 Chirality : 0.034 0.136 1891 Planarity : 0.003 0.028 1211 Dihedral : 29.832 172.220 3430 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.50 % Allowed : 17.86 % Favored : 81.64 % 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: 1.98 (0.31), residues: 748 helix: 2.38 (0.23), residues: 494 sheet: None (None), residues: 0 loop : -0.90 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 131 PHE 0.030 0.002 PHE C 152 TYR 0.017 0.002 TYR D 81 ARG 0.002 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.838 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 84 average time/residue: 0.2442 time to fit residues: 29.7564 Evaluate side-chains 76 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.832 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1093 time to fit residues: 1.2737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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: 0.7793 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 11312 Z= 0.354 Angle : 0.642 7.477 16289 Z= 0.371 Chirality : 0.038 0.160 1891 Planarity : 0.004 0.030 1211 Dihedral : 30.024 171.518 3430 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.67 % Allowed : 19.20 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.75 (0.31), residues: 748 helix: 2.17 (0.23), residues: 494 sheet: None (None), residues: 0 loop : -0.93 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 34 PHE 0.046 0.003 PHE C 152 TYR 0.022 0.002 TYR D 81 ARG 0.003 0.000 ARG F 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.856 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 71 average time/residue: 0.2435 time to fit residues: 24.6604 Evaluate side-chains 75 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.845 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1054 time to fit residues: 1.7847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.129306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.094148 restraints weight = 17698.087| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.21 r_work: 0.3149 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11312 Z= 0.181 Angle : 0.547 7.154 16289 Z= 0.326 Chirality : 0.033 0.135 1891 Planarity : 0.003 0.027 1211 Dihedral : 29.763 171.033 3430 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.83 % Allowed : 18.36 % Favored : 80.80 % 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: 2.18 (0.31), residues: 748 helix: 2.54 (0.23), residues: 494 sheet: None (None), residues: 0 loop : -0.85 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 55 PHE 0.024 0.002 PHE G 152 TYR 0.014 0.001 TYR D 81 ARG 0.001 0.000 ARG A 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1736.51 seconds wall clock time: 32 minutes 31.91 seconds (1951.91 seconds total)