Starting phenix.real_space_refine (version: dev) on Mon Feb 20 04:16:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2023/5u4j_8506_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2023/5u4j_8506.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2023/5u4j_8506_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2023/5u4j_8506_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2023/5u4j_8506_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2023/5u4j_8506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2023/5u4j_8506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2023/5u4j_8506_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u4j_8506/02_2023/5u4j_8506_neut_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "c GLU 152": "OE1" <-> "OE2" Residue "c GLU 161": "OE1" <-> "OE2" Residue "c GLU 166": "OE1" <-> "OE2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "e GLU 55": "OE1" <-> "OE2" Residue "e GLU 65": "OE1" <-> "OE2" Residue "e GLU 145": "OE1" <-> "OE2" Residue "l GLU 25": "OE1" <-> "OE2" Residue "l ARG 56": "NH1" <-> "NH2" Residue "l PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 70": "OE1" <-> "OE2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "v ARG 150": "NH1" <-> "NH2" Residue "v TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 154": "NH1" <-> "NH2" Residue "v ARG 213": "NH1" <-> "NH2" Residue "v GLU 299": "OE1" <-> "OE2" Residue "v GLU 306": "OE1" <-> "OE2" Residue "w ARG 26": "NH1" <-> "NH2" Residue "w GLU 30": "OE1" <-> "OE2" Residue "w ARG 41": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11360 Number of models: 1 Model: "" Number of chains: 10 Chain: "a" Number of atoms: 6591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 6591 Classifications: {'RNA': 307} Modifications used: {'rna2p': 1, 'rna2p_pur': 23, 'rna2p_pyr': 19, 'rna3p': 7, 'rna3p_pur': 144, 'rna3p_pyr': 113} Link IDs: {'rna2p': 43, 'rna3p': 263} Chain breaks: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 233 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 2, 'rna3p': 2, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "c" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 169 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "d" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 523 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "e" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1001 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "z" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 1} Link IDs: {'rna3p': 5} Chain: "x" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 315 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 9} Link IDs: {'rna3p': 14} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "v" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1054 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "w" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Time building chain proxies: 7.14, per 1000 atoms: 0.63 Number of scatterers: 11360 At special positions: 0 Unit cell: (102.598, 114.528, 102.598, 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 15 16.00 P 339 15.00 O 3103 8.00 N 2109 7.00 C 5794 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: 6.58 Conformation dependent library (CDL) restraints added in 748.1 milliseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 934 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 5 sheets defined 22.9% alpha, 21.8% beta 97 base pairs and 206 stacking pairs defined. Time for finding SS restraints: 5.79 Creating SS restraints... Processing helix chain 'd' and resid 8 through 15 removed outlier: 3.743A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG d 14 " --> pdb=" O LYS d 10 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU d 15 " --> pdb=" O LEU d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 31 No H-bonds generated for 'chain 'd' and resid 28 through 31' Processing helix chain 'd' and resid 50 through 64 removed outlier: 3.722A pdb=" N GLN d 54 " --> pdb=" O ASP d 50 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL d 61 " --> pdb=" O GLU d 57 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG d 62 " --> pdb=" O LYS d 58 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE d 64 " --> pdb=" O LYS d 60 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 68 removed outlier: 3.665A pdb=" N GLN e 61 " --> pdb=" O PRO e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 118 removed outlier: 4.027A pdb=" N VAL e 114 " --> pdb=" O ALA e 110 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL e 117 " --> pdb=" O ALA e 113 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 144 removed outlier: 4.108A pdb=" N ARG e 138 " --> pdb=" O ILE e 134 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 9 removed outlier: 3.803A pdb=" N ARG l 9 " --> pdb=" O ASN l 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 140 through 159 removed outlier: 3.544A pdb=" N ARG v 159 " --> pdb=" O TRP v 155 " (cutoff:3.500A) Processing helix chain 'v' and resid 188 through 191 No H-bonds generated for 'chain 'v' and resid 188 through 191' Processing helix chain 'v' and resid 297 through 315 Processing helix chain 'w' and resid 15 through 20 Processing helix chain 'w' and resid 23 through 25 No H-bonds generated for 'chain 'w' and resid 23 through 25' Processing sheet with id= A, first strand: chain 'c' and resid 151 through 155 Processing sheet with id= B, first strand: chain 'e' and resid 46 through 50 removed outlier: 3.809A pdb=" N ALA e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL e 38 " --> pdb=" O LEU e 15 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N GLY e 40 " --> pdb=" O GLU e 13 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLU e 13 " --> pdb=" O GLY e 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'e' and resid 85 through 89 Processing sheet with id= D, first strand: chain 'l' and resid 79 through 82 removed outlier: 6.665A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL l 37 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL l 52 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR l 39 " --> pdb=" O ARG l 50 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG l 50 " --> pdb=" O THR l 39 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'v' and resid 322 through 326 removed outlier: 8.022A pdb=" N VAL v 198 " --> pdb=" O ILE v 323 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER v 325 " --> pdb=" O VAL v 198 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG v 200 " --> pdb=" O SER v 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY v 197 " --> pdb=" O ALA v 220 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE v 217 " --> pdb=" O GLY v 135 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY v 135 " --> pdb=" O PHE v 217 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS v 182 " --> pdb=" O ILE v 165 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ILE v 165 " --> pdb=" O LYS v 182 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N SER v 184 " --> pdb=" O THR v 163 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR v 163 " --> pdb=" O SER v 184 " (cutoff:3.500A) 121 hydrogen bonds defined for protein. 342 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 240 hydrogen bonds 396 hydrogen bond angles 0 basepair planarities 97 basepair parallelities 206 stacking parallelities Total time for adding SS restraints: 5.58 Time building geometry restraints manager: 6.76 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: 2289 1.34 - 1.45: 4498 1.45 - 1.57: 4797 1.57 - 1.69: 670 1.69 - 1.81: 24 Bond restraints: 12278 Sorted by residual: bond pdb=" N3 G7M a 527 " pdb=" C4 G7M a 527 " ideal model delta sigma weight residual 1.492 1.342 0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C2 4OC a1402 " pdb=" N3 4OC a1402 " ideal model delta sigma weight residual 1.507 1.359 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" C2 5MC a1407 " pdb=" N3 5MC a1407 " ideal model delta sigma weight residual 1.493 1.354 0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" P G7M a 527 " pdb=" OP1 G7M a 527 " ideal model delta sigma weight residual 1.510 1.649 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" N3 2MG a1516 " pdb=" C4 2MG a1516 " ideal model delta sigma weight residual 1.496 1.360 0.136 2.00e-02 2.50e+03 4.62e+01 ... (remaining 12273 not shown) Histogram of bond angle deviations from ideal: 97.09 - 104.93: 1491 104.93 - 112.77: 6840 112.77 - 120.61: 5574 120.61 - 128.45: 3799 128.45 - 136.30: 503 Bond angle restraints: 18207 Sorted by residual: angle pdb=" O3' G7M a 527 " pdb=" P C a 528 " pdb=" O5' C a 528 " ideal model delta sigma weight residual 104.00 122.87 -18.87 1.50e+00 4.44e-01 1.58e+02 angle pdb=" C1' G7M a 527 " pdb=" N9 G7M a 527 " pdb=" C8 G7M a 527 " ideal model delta sigma weight residual 94.96 129.44 -34.48 3.00e+00 1.11e-01 1.32e+02 angle pdb=" O3' G a1064 " pdb=" C3' G a1064 " pdb=" C2' G a1064 " ideal model delta sigma weight residual 109.50 121.44 -11.94 1.50e+00 4.44e-01 6.34e+01 angle pdb=" N LYS w 8 " pdb=" CA LYS w 8 " pdb=" C LYS w 8 " ideal model delta sigma weight residual 110.97 102.56 8.41 1.09e+00 8.42e-01 5.95e+01 angle pdb=" C4' A a 533 " pdb=" C3' A a 533 " pdb=" O3' A a 533 " ideal model delta sigma weight residual 109.40 120.28 -10.88 1.50e+00 4.44e-01 5.26e+01 ... (remaining 18202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 6215 35.82 - 71.64: 279 71.64 - 107.47: 24 107.47 - 143.29: 4 143.29 - 179.11: 5 Dihedral angle restraints: 6527 sinusoidal: 5057 harmonic: 1470 Sorted by residual: dihedral pdb=" C5' A a 560 " pdb=" C4' A a 560 " pdb=" C3' A a 560 " pdb=" O3' A a 560 " ideal model delta sinusoidal sigma weight residual 147.00 82.18 64.82 1 8.00e+00 1.56e-02 8.62e+01 dihedral pdb=" C4' A a 560 " pdb=" C3' A a 560 " pdb=" C2' A a 560 " pdb=" C1' A a 560 " ideal model delta sinusoidal sigma weight residual -35.00 26.81 -61.81 1 8.00e+00 1.56e-02 7.91e+01 dihedral pdb=" O4' A a 560 " pdb=" C4' A a 560 " pdb=" C3' A a 560 " pdb=" C2' A a 560 " ideal model delta sinusoidal sigma weight residual 24.00 -29.69 53.69 1 8.00e+00 1.56e-02 6.12e+01 ... (remaining 6524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 2160 0.202 - 0.405: 107 0.405 - 0.607: 2 0.607 - 0.809: 3 0.809 - 1.012: 1 Chirality restraints: 2273 Sorted by residual: chirality pdb=" P C a 528 " pdb=" OP1 C a 528 " pdb=" OP2 C a 528 " pdb=" O5' C a 528 " both_signs ideal model delta sigma weight residual True 2.41 -3.42 -1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" C3' G a1064 " pdb=" C4' G a1064 " pdb=" O3' G a1064 " pdb=" C2' G a1064 " both_signs ideal model delta sigma weight residual False -2.74 -1.97 -0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" C3' A a 913 " pdb=" C4' A a 913 " pdb=" O3' A a 913 " pdb=" C2' A a 913 " both_signs ideal model delta sigma weight residual False -2.74 -2.04 -0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 2270 not shown) Planarity restraints: 1065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " 0.085 2.00e-02 2.50e+03 5.03e-01 5.70e+03 pdb=" C4' 5MC a1407 " -0.434 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " -0.597 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " 0.529 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " 0.409 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " 0.246 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " -0.745 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " -0.264 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " 0.772 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1516 " 0.023 2.00e-02 2.50e+03 4.80e-01 5.18e+03 pdb=" C4' 2MG a1516 " -0.385 2.00e-02 2.50e+03 pdb=" O4' 2MG a1516 " -0.473 2.00e-02 2.50e+03 pdb=" C3' 2MG a1516 " 0.563 2.00e-02 2.50e+03 pdb=" O3' 2MG a1516 " 0.387 2.00e-02 2.50e+03 pdb=" C2' 2MG a1516 " 0.233 2.00e-02 2.50e+03 pdb=" O2' 2MG a1516 " -0.765 2.00e-02 2.50e+03 pdb=" C1' 2MG a1516 " -0.294 2.00e-02 2.50e+03 pdb=" N9 2MG a1516 " 0.711 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 a1519 " 0.123 2.00e-02 2.50e+03 2.01e-01 4.02e+02 pdb=" N6 MA6 a1519 " -0.347 2.00e-02 2.50e+03 pdb=" C10 MA6 a1519 " 0.114 2.00e-02 2.50e+03 pdb=" C9 MA6 a1519 " 0.110 2.00e-02 2.50e+03 ... (remaining 1062 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 3 2.42 - 3.04: 4989 3.04 - 3.66: 20366 3.66 - 4.28: 30802 4.28 - 4.90: 42361 Nonbonded interactions: 98521 Sorted by model distance: nonbonded pdb=" N4 C a 528 " pdb=" OD1 ASN l 46 " model vdw 1.797 2.520 nonbonded pdb=" CB LYS l 44 " pdb=" CD PRO l 45 " model vdw 2.219 3.840 nonbonded pdb=" O GLY e 108 " pdb=" N ARG e 112 " model vdw 2.249 2.520 nonbonded pdb=" CE LYS w 8 " pdb=" O HIS w 21 " model vdw 2.448 3.440 nonbonded pdb=" O2' U a 921 " pdb=" O THR e 24 " model vdw 2.505 2.440 ... (remaining 98516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 339 5.49 5 S 15 5.16 5 C 5794 2.51 5 N 2109 2.21 5 O 3103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 13.060 Check model and map are aligned: 0.150 Process input model: 40.140 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.100 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 0.009 0.150 12278 Z= 0.546 Angle : 1.213 34.477 18207 Z= 0.753 Chirality : 0.103 1.012 2273 Planarity : 0.023 0.503 1065 Dihedral : 17.201 179.111 5593 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.69 % Favored : 93.92 % Rotamer Outliers : 2.82 % Cbeta Deviations : 0.43 % 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: -2.95 (0.28), residues: 510 helix: -2.54 (0.31), residues: 110 sheet: -0.97 (0.40), residues: 133 loop : -2.22 (0.27), residues: 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 133 average time/residue: 0.3565 time to fit residues: 61.3259 Evaluate side-chains 112 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 0.682 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1468 time to fit residues: 1.5883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 36 GLN v 214 HIS w 5 GLN w 21 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 12278 Z= 0.215 Angle : 0.739 13.463 18207 Z= 0.405 Chirality : 0.040 0.281 2273 Planarity : 0.007 0.120 1065 Dihedral : 15.576 173.085 4579 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.35 % Favored : 97.45 % Rotamer Outliers : 1.88 % 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: -1.67 (0.32), residues: 510 helix: 0.15 (0.44), residues: 121 sheet: -0.53 (0.41), residues: 137 loop : -2.12 (0.29), residues: 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 117 average time/residue: 0.3469 time to fit residues: 52.7385 Evaluate side-chains 113 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1013 time to fit residues: 1.6497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 29 GLN w 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12278 Z= 0.203 Angle : 0.676 12.231 18207 Z= 0.378 Chirality : 0.036 0.254 2273 Planarity : 0.007 0.120 1065 Dihedral : 15.160 174.808 4579 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.92 % Favored : 95.88 % Rotamer Outliers : 3.76 % 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: -1.40 (0.33), residues: 510 helix: 0.53 (0.46), residues: 126 sheet: -0.54 (0.41), residues: 137 loop : -1.97 (0.31), residues: 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 137 average time/residue: 0.3222 time to fit residues: 57.6704 Evaluate side-chains 132 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1133 time to fit residues: 2.4788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 12278 Z= 0.382 Angle : 0.785 12.434 18207 Z= 0.422 Chirality : 0.041 0.290 2273 Planarity : 0.007 0.122 1065 Dihedral : 15.343 177.111 4579 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.12 % Favored : 95.69 % Rotamer Outliers : 2.35 % 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: -1.39 (0.33), residues: 510 helix: 0.33 (0.43), residues: 127 sheet: -0.42 (0.42), residues: 137 loop : -1.92 (0.33), residues: 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 135 average time/residue: 0.3611 time to fit residues: 63.0711 Evaluate side-chains 128 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 0.732 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1133 time to fit residues: 2.0676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 0.0770 chunk 67 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 12278 Z= 0.193 Angle : 0.668 12.221 18207 Z= 0.375 Chirality : 0.035 0.253 2273 Planarity : 0.007 0.119 1065 Dihedral : 15.064 177.755 4579 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.16 % Favored : 97.65 % Rotamer Outliers : 2.35 % 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: -1.10 (0.35), residues: 510 helix: 0.80 (0.45), residues: 127 sheet: -0.51 (0.42), residues: 147 loop : -1.72 (0.35), residues: 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 129 average time/residue: 0.3465 time to fit residues: 57.9831 Evaluate side-chains 127 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 0.748 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1038 time to fit residues: 1.9996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 0.0870 chunk 6 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12278 Z= 0.189 Angle : 0.660 12.153 18207 Z= 0.371 Chirality : 0.034 0.257 2273 Planarity : 0.007 0.120 1065 Dihedral : 14.975 178.496 4579 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.14 % Favored : 96.67 % Rotamer Outliers : 1.18 % 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: -1.03 (0.35), residues: 510 helix: 0.79 (0.45), residues: 129 sheet: -0.35 (0.41), residues: 143 loop : -1.75 (0.35), residues: 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 122 average time/residue: 0.3357 time to fit residues: 53.7994 Evaluate side-chains 125 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 0.798 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1832 time to fit residues: 2.2825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 12278 Z= 0.292 Angle : 0.729 12.155 18207 Z= 0.399 Chirality : 0.037 0.273 2273 Planarity : 0.007 0.121 1065 Dihedral : 15.038 179.235 4579 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.53 % Favored : 96.27 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.34), residues: 510 helix: 0.63 (0.44), residues: 129 sheet: -0.41 (0.41), residues: 145 loop : -1.77 (0.35), residues: 236 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 121 average time/residue: 0.3363 time to fit residues: 52.9915 Evaluate side-chains 124 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1311 time to fit residues: 2.4987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 50 optimal weight: 0.2980 chunk 53 optimal weight: 0.0000 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 12278 Z= 0.147 Angle : 0.635 12.221 18207 Z= 0.361 Chirality : 0.032 0.244 2273 Planarity : 0.007 0.118 1065 Dihedral : 14.776 179.657 4579 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.16 % Favored : 97.65 % Rotamer Outliers : 0.47 % 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: -1.07 (0.35), residues: 510 helix: 0.74 (0.45), residues: 129 sheet: -0.59 (0.41), residues: 143 loop : -1.59 (0.36), residues: 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 124 average time/residue: 0.4115 time to fit residues: 64.6400 Evaluate side-chains 120 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1052 time to fit residues: 1.2293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 57 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 12278 Z= 0.168 Angle : 0.645 12.180 18207 Z= 0.364 Chirality : 0.032 0.266 2273 Planarity : 0.007 0.119 1065 Dihedral : 14.718 179.979 4579 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.33 % Favored : 96.47 % Rotamer Outliers : 0.94 % 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: -1.09 (0.34), residues: 510 helix: 0.83 (0.45), residues: 127 sheet: -0.58 (0.41), residues: 143 loop : -1.66 (0.35), residues: 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 124 average time/residue: 0.3708 time to fit residues: 59.4575 Evaluate side-chains 126 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 0.733 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1000 time to fit residues: 1.4392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.0010 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 96 HIS ** v 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12278 Z= 0.166 Angle : 0.641 12.147 18207 Z= 0.362 Chirality : 0.032 0.265 2273 Planarity : 0.007 0.119 1065 Dihedral : 14.671 179.526 4579 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.35 % Favored : 97.45 % Rotamer Outliers : 0.47 % 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: -0.97 (0.34), residues: 510 helix: 1.08 (0.46), residues: 124 sheet: -0.58 (0.41), residues: 142 loop : -1.61 (0.34), residues: 244 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 126 average time/residue: 0.3692 time to fit residues: 59.1235 Evaluate side-chains 111 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1005 time to fit residues: 1.0270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.159969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.136666 restraints weight = 16241.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.140249 restraints weight = 5825.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.142400 restraints weight = 3367.099| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 12278 Z= 0.342 Angle : 0.788 12.341 18207 Z= 0.423 Chirality : 0.038 0.283 2273 Planarity : 0.008 0.123 1065 Dihedral : 15.097 178.734 4579 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.29 % Favored : 94.51 % Rotamer Outliers : 1.41 % 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: -1.41 (0.34), residues: 510 helix: 0.34 (0.45), residues: 126 sheet: -0.59 (0.42), residues: 139 loop : -1.83 (0.34), residues: 245 =============================================================================== Job complete usr+sys time: 2037.82 seconds wall clock time: 38 minutes 49.51 seconds (2329.51 seconds total)