Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 12:16:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/04_2023/6vp0_21302_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/04_2023/6vp0_21302.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/04_2023/6vp0_21302_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/04_2023/6vp0_21302_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/04_2023/6vp0_21302_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/04_2023/6vp0_21302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/04_2023/6vp0_21302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/04_2023/6vp0_21302_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp0_21302/04_2023/6vp0_21302_updated.pdb" } resolution = 3.1 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= 0.005 sd= 0.145 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 14 5.49 5 S 44 5.16 5 C 4796 2.51 5 N 1146 2.21 5 O 1210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 127": "OD1" <-> "OD2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 127": "OD1" <-> "OD2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7210 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3353 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 385} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3353 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 385} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 252 Unusual residues: {'3VV': 1, 'AV0': 1, 'POV': 2} Classifications: {'peptide': 2, 'undetermined': 4} Link IDs: {'TRANS': 1, None: 4} Not linked: pdbres="POV C 601 " pdbres="P5S C 602 " Not linked: pdbres="P5S C 603 " pdbres="POV C 604 " Not linked: pdbres="POV C 604 " pdbres="3VV C 605 " Not linked: pdbres="3VV C 605 " pdbres="AV0 C 606 " Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 252 Unusual residues: {'3VV': 1, 'AV0': 1, 'POV': 2} Classifications: {'peptide': 2, 'undetermined': 4} Link IDs: {'TRANS': 1, None: 4} Not linked: pdbres="POV E 601 " pdbres="P5S E 602 " Not linked: pdbres="P5S E 603 " pdbres="POV E 604 " Not linked: pdbres="POV E 604 " pdbres="3VV E 605 " Not linked: pdbres="3VV E 605 " pdbres="AV0 E 606 " Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 4.79, per 1000 atoms: 0.66 Number of scatterers: 7210 At special positions: 0 Unit cell: (79.094, 123.654, 75.752, 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 44 16.00 P 14 15.00 O 1210 8.00 N 1146 7.00 C 4796 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: 3.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 0 sheets defined 73.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 86 through 114 removed outlier: 5.803A pdb=" N ARG C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 126 Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 132 through 155 removed outlier: 4.713A pdb=" N ASN C 141 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 185 Proline residue: C 179 - end of helix Processing helix chain 'C' and resid 193 through 222 Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 275 through 306 removed outlier: 5.074A pdb=" N VAL C 301 " --> pdb=" O GLN C 297 " (cutoff:3.500A) Proline residue: C 302 - end of helix Processing helix chain 'C' and resid 316 through 342 removed outlier: 3.877A pdb=" N LYS C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Proline residue: C 329 - end of helix Processing helix chain 'C' and resid 344 through 353 Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 370 through 376 Processing helix chain 'C' and resid 379 through 388 Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'C' and resid 400 through 423 removed outlier: 4.168A pdb=" N VAL C 421 " --> pdb=" O TYR C 417 " (cutoff:3.500A) Proline residue: C 422 - end of helix Processing helix chain 'C' and resid 429 through 447 removed outlier: 4.191A pdb=" N ILE C 438 " --> pdb=" O MET C 434 " (cutoff:3.500A) Proline residue: C 439 - end of helix Processing helix chain 'C' and resid 451 through 462 removed outlier: 3.576A pdb=" N ILE C 462 " --> pdb=" O TRP C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 480 removed outlier: 3.861A pdb=" N TYR C 472 " --> pdb=" O ALA C 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'E' and resid 86 through 114 removed outlier: 5.803A pdb=" N ARG E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU E 103 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 128 through 130 No H-bonds generated for 'chain 'E' and resid 128 through 130' Processing helix chain 'E' and resid 132 through 155 removed outlier: 4.713A pdb=" N ASN E 141 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE E 143 " --> pdb=" O ALA E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 185 Proline residue: E 179 - end of helix Processing helix chain 'E' and resid 193 through 222 Processing helix chain 'E' and resid 249 through 256 Processing helix chain 'E' and resid 275 through 306 removed outlier: 5.074A pdb=" N VAL E 301 " --> pdb=" O GLN E 297 " (cutoff:3.500A) Proline residue: E 302 - end of helix Processing helix chain 'E' and resid 316 through 342 removed outlier: 3.877A pdb=" N LYS E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 326 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Proline residue: E 329 - end of helix Processing helix chain 'E' and resid 344 through 353 Processing helix chain 'E' and resid 364 through 366 No H-bonds generated for 'chain 'E' and resid 364 through 366' Processing helix chain 'E' and resid 370 through 376 Processing helix chain 'E' and resid 379 through 388 Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 400 through 423 removed outlier: 4.168A pdb=" N VAL E 421 " --> pdb=" O TYR E 417 " (cutoff:3.500A) Proline residue: E 422 - end of helix Processing helix chain 'E' and resid 429 through 447 removed outlier: 4.191A pdb=" N ILE E 438 " --> pdb=" O MET E 434 " (cutoff:3.500A) Proline residue: E 439 - end of helix Processing helix chain 'E' and resid 451 through 462 removed outlier: 3.576A pdb=" N ILE E 462 " --> pdb=" O TRP E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 480 removed outlier: 3.861A pdb=" N TYR E 472 " --> pdb=" O ALA E 468 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1064 1.32 - 1.45: 2202 1.45 - 1.57: 4058 1.57 - 1.69: 26 1.69 - 1.82: 72 Bond restraints: 7422 Sorted by residual: bond pdb=" C49 3VV C 605 " pdb=" C50 3VV C 605 " ideal model delta sigma weight residual 1.291 1.527 -0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C49 3VV E 605 " pdb=" C50 3VV E 605 " ideal model delta sigma weight residual 1.291 1.527 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C49 3VV C 605 " pdb=" O48 3VV C 605 " ideal model delta sigma weight residual 1.621 1.416 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C49 3VV E 605 " pdb=" O48 3VV E 605 " ideal model delta sigma weight residual 1.621 1.416 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C47 3VV E 605 " pdb=" O48 3VV E 605 " ideal model delta sigma weight residual 1.286 1.446 -0.160 2.00e-02 2.50e+03 6.42e+01 ... (remaining 7417 not shown) Histogram of bond angle deviations from ideal: 67.40 - 80.73: 4 80.73 - 94.07: 8 94.07 - 107.41: 342 107.41 - 120.75: 7584 120.75 - 134.09: 2108 Bond angle restraints: 10046 Sorted by residual: angle pdb=" OG P5S E 603 " pdb=" P12 P5S E 603 " pdb=" O16 P5S E 603 " ideal model delta sigma weight residual 98.42 67.40 31.02 3.00e+00 1.11e-01 1.07e+02 angle pdb=" OG P5S C 603 " pdb=" P12 P5S C 603 " pdb=" O16 P5S C 603 " ideal model delta sigma weight residual 98.42 67.42 31.00 3.00e+00 1.11e-01 1.07e+02 angle pdb=" OG P5S E 602 " pdb=" P12 P5S E 602 " pdb=" O13 P5S E 602 " ideal model delta sigma weight residual 111.99 82.86 29.13 3.00e+00 1.11e-01 9.43e+01 angle pdb=" OG P5S C 602 " pdb=" P12 P5S C 602 " pdb=" O13 P5S C 602 " ideal model delta sigma weight residual 111.99 82.87 29.12 3.00e+00 1.11e-01 9.42e+01 angle pdb=" OG P5S C 602 " pdb=" P12 P5S C 602 " pdb=" O16 P5S C 602 " ideal model delta sigma weight residual 98.42 69.46 28.96 3.00e+00 1.11e-01 9.32e+01 ... (remaining 10041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.58: 3967 26.58 - 53.16: 237 53.16 - 79.74: 32 79.74 - 106.32: 6 106.32 - 132.90: 18 Dihedral angle restraints: 4260 sinusoidal: 1852 harmonic: 2408 Sorted by residual: dihedral pdb=" C22 P5S E 602 " pdb=" C23 P5S E 602 " pdb=" C24 P5S E 602 " pdb=" C25 P5S E 602 " ideal model delta sinusoidal sigma weight residual -179.61 -46.71 -132.90 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" C22 P5S C 602 " pdb=" C23 P5S C 602 " pdb=" C24 P5S C 602 " pdb=" C25 P5S C 602 " ideal model delta sinusoidal sigma weight residual -179.61 -46.72 -132.89 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" CB P5S E 602 " pdb=" OG P5S E 602 " pdb=" P12 P5S E 602 " pdb=" O16 P5S E 602 " ideal model delta sinusoidal sigma weight residual 150.82 -76.41 -132.77 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 4257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 988 0.077 - 0.154: 66 0.154 - 0.231: 3 0.231 - 0.308: 5 0.308 - 0.385: 4 Chirality restraints: 1066 Sorted by residual: chirality pdb=" C31 3VV C 605 " pdb=" C29 3VV C 605 " pdb=" C33 3VV C 605 " pdb=" O32 3VV C 605 " both_signs ideal model delta sigma weight residual False -2.53 -2.15 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" C31 3VV E 605 " pdb=" C29 3VV E 605 " pdb=" C33 3VV E 605 " pdb=" O32 3VV E 605 " both_signs ideal model delta sigma weight residual False -2.53 -2.15 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C50 3VV C 605 " pdb=" C49 3VV C 605 " pdb=" C52 3VV C 605 " pdb=" O51 3VV C 605 " both_signs ideal model delta sigma weight residual False -2.38 -2.70 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1063 not shown) Planarity restraints: 1188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C27 3VV C 605 " -0.039 2.00e-02 2.50e+03 3.22e-02 1.29e+01 pdb=" C29 3VV C 605 " 0.018 2.00e-02 2.50e+03 pdb=" C31 3VV C 605 " -0.031 2.00e-02 2.50e+03 pdb=" N28 3VV C 605 " 0.048 2.00e-02 2.50e+03 pdb=" O30 3VV C 605 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 3VV E 605 " 0.039 2.00e-02 2.50e+03 3.18e-02 1.27e+01 pdb=" C29 3VV E 605 " -0.018 2.00e-02 2.50e+03 pdb=" C31 3VV E 605 " 0.031 2.00e-02 2.50e+03 pdb=" N28 3VV E 605 " -0.048 2.00e-02 2.50e+03 pdb=" O30 3VV E 605 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 391 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO C 392 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 392 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 392 " 0.020 5.00e-02 4.00e+02 ... (remaining 1185 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2289 2.83 - 3.35: 6753 3.35 - 3.87: 11598 3.87 - 4.38: 13277 4.38 - 4.90: 23517 Nonbonded interactions: 57434 Sorted by model distance: nonbonded pdb=" NH2 ARG C 67 " pdb=" O HIS C 69 " model vdw 2.316 2.520 nonbonded pdb=" NH2 ARG E 67 " pdb=" O HIS E 69 " model vdw 2.316 2.520 nonbonded pdb=" N ASP C 245 " pdb=" OD1 ASP C 245 " model vdw 2.329 2.520 nonbonded pdb=" N ASP E 245 " pdb=" OD1 ASP E 245 " model vdw 2.329 2.520 nonbonded pdb=" ND1 HIS C 382 " pdb=" O39 3VV C 605 " model vdw 2.339 2.520 ... (remaining 57429 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 'C' selection = chain 'E' } 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.380 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.040 Find NCS groups from input model: 0.390 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: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 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 : 0.011 0.236 7422 Z= 0.620 Angle : 1.374 31.024 10046 Z= 0.521 Chirality : 0.050 0.385 1066 Planarity : 0.004 0.034 1188 Dihedral : 19.193 132.898 2696 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer Outliers : 1.96 % 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: -1.11 (0.26), residues: 800 helix: -0.13 (0.19), residues: 598 sheet: None (None), residues: 0 loop : -2.32 (0.35), residues: 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 0.830 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 152 average time/residue: 0.2832 time to fit residues: 53.6392 Evaluate side-chains 102 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0690 time to fit residues: 1.7778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN C 201 HIS C 246 ASN C 292 GLN E 149 GLN E 201 HIS E 246 ASN E 292 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 7422 Z= 0.166 Angle : 0.512 5.299 10046 Z= 0.245 Chirality : 0.037 0.118 1066 Planarity : 0.004 0.041 1188 Dihedral : 17.278 118.950 1148 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 2.80 % 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: 0.91 (0.29), residues: 800 helix: 1.46 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -1.95 (0.36), residues: 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 0.837 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 118 average time/residue: 0.2591 time to fit residues: 38.7081 Evaluate side-chains 114 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0766 time to fit residues: 2.4271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 415 HIS C 465 GLN E 415 HIS E 465 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 7422 Z= 0.307 Angle : 0.562 5.461 10046 Z= 0.277 Chirality : 0.040 0.124 1066 Planarity : 0.004 0.040 1188 Dihedral : 16.487 121.075 1148 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 1.12 % 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 (0.29), residues: 800 helix: 1.75 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -1.57 (0.38), residues: 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 0.811 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 114 average time/residue: 0.2312 time to fit residues: 34.3694 Evaluate side-chains 114 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 0.818 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1209 time to fit residues: 1.9917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.7451 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 7422 Z= 0.293 Angle : 0.548 5.601 10046 Z= 0.270 Chirality : 0.040 0.121 1066 Planarity : 0.004 0.039 1188 Dihedral : 16.106 121.242 1148 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 1.96 % 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: 1.68 (0.29), residues: 800 helix: 1.91 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -1.32 (0.39), residues: 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 0.892 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 121 average time/residue: 0.2198 time to fit residues: 35.2832 Evaluate side-chains 114 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.826 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0762 time to fit residues: 1.9891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 0.1980 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7422 Z= 0.194 Angle : 0.499 5.456 10046 Z= 0.246 Chirality : 0.038 0.115 1066 Planarity : 0.004 0.040 1188 Dihedral : 15.546 117.500 1148 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.98 % 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: 2.06 (0.30), residues: 800 helix: 2.23 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -1.35 (0.40), residues: 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.748 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 121 average time/residue: 0.2226 time to fit residues: 35.1222 Evaluate side-chains 112 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0650 time to fit residues: 1.2517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.0050 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 7422 Z= 0.142 Angle : 0.491 6.071 10046 Z= 0.238 Chirality : 0.037 0.114 1066 Planarity : 0.004 0.040 1188 Dihedral : 15.087 113.323 1148 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.30), residues: 800 helix: 2.43 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -1.29 (0.39), residues: 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 0.751 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 110 average time/residue: 0.2363 time to fit residues: 33.8577 Evaluate side-chains 106 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.0000 chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 292 GLN E 215 ASN E 292 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 7422 Z= 0.152 Angle : 0.496 7.157 10046 Z= 0.240 Chirality : 0.037 0.115 1066 Planarity : 0.004 0.040 1188 Dihedral : 14.686 112.083 1148 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 0.42 % 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: 2.40 (0.30), residues: 800 helix: 2.49 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -1.27 (0.38), residues: 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 0.799 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 113 average time/residue: 0.2433 time to fit residues: 36.0049 Evaluate side-chains 108 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.824 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 49 optimal weight: 0.0070 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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: 0.7372 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 7422 Z= 0.144 Angle : 0.493 8.552 10046 Z= 0.237 Chirality : 0.037 0.114 1066 Planarity : 0.004 0.040 1188 Dihedral : 14.255 109.731 1148 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.30), residues: 800 helix: 2.53 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.04 (0.38), residues: 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 0.878 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 106 average time/residue: 0.2461 time to fit residues: 33.9032 Evaluate side-chains 109 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1025 time to fit residues: 1.9273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 22 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 ASN E 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 7422 Z= 0.150 Angle : 0.499 8.220 10046 Z= 0.241 Chirality : 0.037 0.130 1066 Planarity : 0.004 0.040 1188 Dihedral : 14.029 108.541 1148 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 0.42 % 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: 2.57 (0.30), residues: 800 helix: 2.51 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -0.96 (0.39), residues: 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.751 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 108 average time/residue: 0.2258 time to fit residues: 31.7102 Evaluate side-chains 104 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1015 time to fit residues: 1.2228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 49 optimal weight: 0.0270 chunk 38 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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: 0.7356 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 7422 Z= 0.136 Angle : 0.491 8.344 10046 Z= 0.236 Chirality : 0.037 0.145 1066 Planarity : 0.003 0.041 1188 Dihedral : 13.704 105.132 1148 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 0.14 % 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: 2.67 (0.30), residues: 800 helix: 2.58 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -0.91 (0.39), residues: 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.798 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 106 average time/residue: 0.2340 time to fit residues: 32.2105 Evaluate side-chains 102 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.829 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1031 time to fit residues: 1.2678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.154920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.121723 restraints weight = 7809.104| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.92 r_work: 0.3240 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7422 Z= 0.172 Angle : 0.510 8.620 10046 Z= 0.247 Chirality : 0.038 0.178 1066 Planarity : 0.004 0.040 1188 Dihedral : 13.690 107.793 1148 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.30), residues: 800 helix: 2.51 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -0.87 (0.40), residues: 198 =============================================================================== Job complete usr+sys time: 1735.22 seconds wall clock time: 32 minutes 3.47 seconds (1923.47 seconds total)