Starting phenix.real_space_refine on Tue Feb 13 04:18:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeu_13941/02_2024/7qeu_13941_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeu_13941/02_2024/7qeu_13941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeu_13941/02_2024/7qeu_13941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeu_13941/02_2024/7qeu_13941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeu_13941/02_2024/7qeu_13941_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeu_13941/02_2024/7qeu_13941_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 2011 2.51 5 N 468 2.21 5 O 495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3002 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1419 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 166} Chain breaks: 1 Chain: "B" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1514 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {'LMT': 2, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {'LMT': 2, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.41, per 1000 atoms: 0.80 Number of scatterers: 3002 At special positions: 0 Unit cell: (71.94, 67.58, 85.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 495 8.00 N 468 7.00 C 2011 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.03 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: 1.21 Conformation dependent library (CDL) restraints added in 522.7 milliseconds 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 690 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 2 sheets defined 70.5% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 19 through 22 No H-bonds generated for 'chain 'A' and resid 19 through 22' Processing helix chain 'A' and resid 24 through 38 Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 73 through 100 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 158 removed outlier: 3.557A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 216 removed outlier: 3.647A pdb=" N ARG A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 14 removed outlier: 3.703A pdb=" N VAL B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 38 removed outlier: 3.850A pdb=" N ILE B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 60 through 68 Processing helix chain 'B' and resid 73 through 100 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 130 through 158 removed outlier: 3.519A pdb=" N VAL B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 216 removed outlier: 3.518A pdb=" N ARG B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 166 through 169 Processing sheet with id= B, first strand: chain 'B' and resid 166 through 169 190 hydrogen bonds defined for protein. 564 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: 0.74 Time building geometry restraints manager: 1.30 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: 865 1.34 - 1.46: 666 1.46 - 1.57: 1502 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 3073 Sorted by residual: bond pdb=" C1 LMT A 301 " pdb=" C2 LMT A 301 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C1 LMT B 402 " pdb=" C2 LMT B 402 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.00e-02 2.50e+03 5.85e+00 bond pdb=" C7 LMT B 401 " pdb=" C8 LMT B 401 " ideal model delta sigma weight residual 1.529 1.567 -0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C7 LMT A 302 " pdb=" C8 LMT A 302 " ideal model delta sigma weight residual 1.529 1.566 -0.037 2.00e-02 2.50e+03 3.44e+00 bond pdb=" C7 LMT B 402 " pdb=" C8 LMT B 402 " ideal model delta sigma weight residual 1.529 1.565 -0.036 2.00e-02 2.50e+03 3.27e+00 ... (remaining 3068 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.34: 66 106.34 - 113.25: 1722 113.25 - 120.16: 1088 120.16 - 127.07: 1239 127.07 - 133.98: 44 Bond angle restraints: 4159 Sorted by residual: angle pdb=" C6 LMT A 302 " pdb=" C7 LMT A 302 " pdb=" C8 LMT A 302 " ideal model delta sigma weight residual 117.26 109.43 7.83 3.00e+00 1.11e-01 6.82e+00 angle pdb=" C6 LMT B 402 " pdb=" C7 LMT B 402 " pdb=" C8 LMT B 402 " ideal model delta sigma weight residual 117.26 109.49 7.77 3.00e+00 1.11e-01 6.71e+00 angle pdb=" C6 LMT A 301 " pdb=" C7 LMT A 301 " pdb=" C8 LMT A 301 " ideal model delta sigma weight residual 117.26 109.62 7.64 3.00e+00 1.11e-01 6.48e+00 angle pdb=" CA ARG B 75 " pdb=" CB ARG B 75 " pdb=" CG ARG B 75 " ideal model delta sigma weight residual 114.10 109.10 5.00 2.00e+00 2.50e-01 6.26e+00 angle pdb=" C6 LMT B 401 " pdb=" C7 LMT B 401 " pdb=" C8 LMT B 401 " ideal model delta sigma weight residual 117.26 109.76 7.50 3.00e+00 1.11e-01 6.25e+00 ... (remaining 4154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.67: 1470 11.67 - 23.33: 199 23.33 - 35.00: 87 35.00 - 46.67: 18 46.67 - 58.33: 9 Dihedral angle restraints: 1783 sinusoidal: 720 harmonic: 1063 Sorted by residual: dihedral pdb=" CA PRO B 175 " pdb=" C PRO B 175 " pdb=" N ASN B 176 " pdb=" CA ASN B 176 " ideal model delta harmonic sigma weight residual 180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA PRO A 175 " pdb=" C PRO A 175 " pdb=" N ASN A 176 " pdb=" CA ASN A 176 " ideal model delta harmonic sigma weight residual -180.00 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CB MET B 34 " pdb=" CG MET B 34 " pdb=" SD MET B 34 " pdb=" CE MET B 34 " ideal model delta sinusoidal sigma weight residual 180.00 123.06 56.94 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 1780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 220 0.028 - 0.055: 174 0.055 - 0.082: 48 0.082 - 0.110: 22 0.110 - 0.137: 7 Chirality restraints: 471 Sorted by residual: chirality pdb=" CA THR A 86 " pdb=" N THR A 86 " pdb=" C THR A 86 " pdb=" CB THR A 86 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA THR B 86 " pdb=" N THR B 86 " pdb=" C THR B 86 " pdb=" CB THR B 86 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA PRO B 173 " pdb=" N PRO B 173 " pdb=" C PRO B 173 " pdb=" CB PRO B 173 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 468 not shown) Planarity restraints: 494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 174 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 175 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 65 " -0.014 2.00e-02 2.50e+03 7.43e-03 1.10e+00 pdb=" CG TYR B 65 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR B 65 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 65 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 65 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 65 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 65 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 65 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 174 " -0.015 5.00e-02 4.00e+02 2.32e-02 8.63e-01 pdb=" N PRO B 175 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 175 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 175 " -0.013 5.00e-02 4.00e+02 ... (remaining 491 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 36 2.69 - 3.24: 2973 3.24 - 3.79: 4407 3.79 - 4.35: 5726 4.35 - 4.90: 9628 Nonbonded interactions: 22770 Sorted by model distance: nonbonded pdb=" O ILE B 71 " pdb=" OH TYR B 158 " model vdw 2.135 2.440 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 158 " model vdw 2.140 2.440 nonbonded pdb=" OH TYR A 68 " pdb=" O LYS A 168 " model vdw 2.260 2.440 nonbonded pdb=" O CYS A 174 " pdb=" O HOH A 401 " model vdw 2.291 2.440 nonbonded pdb=" O THR B 135 " pdb=" OG SER B 138 " model vdw 2.295 2.440 ... (remaining 22765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 217 or (resid 301 and (name C4 or name C5 or na \ me C6 or name C7 or name C8 )) or resid 302 through 303)) selection = (chain 'B' and (resid 18 through 217 or resid 401 or (resid 402 and (name C3 or \ name C4 or name C5 or name C6 or name C7 or name C8 )) or (resid 403 and (name C \ 11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C18 or na \ me C19 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C8 )))) } 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: 0.260 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: 1.390 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.710 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 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:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 3073 Z= 0.473 Angle : 0.798 7.832 4159 Z= 0.375 Chirality : 0.043 0.137 471 Planarity : 0.003 0.029 494 Dihedral : 13.541 58.333 1075 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.76 (0.43), residues: 351 helix: 0.99 (0.32), residues: 236 sheet: 1.25 (1.08), residues: 22 loop : -0.78 (0.67), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 24 HIS 0.002 0.001 HIS A 73 PHE 0.013 0.001 PHE A 181 TYR 0.014 0.002 TYR B 65 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.325 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 1.4979 time to fit residues: 55.3035 Evaluate side-chains 30 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 21 optimal weight: 0.0020 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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: 0.8489 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3073 Z= 0.184 Angle : 0.544 6.952 4159 Z= 0.294 Chirality : 0.041 0.135 471 Planarity : 0.004 0.030 494 Dihedral : 7.190 53.094 426 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.93 % Allowed : 7.12 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.47), residues: 351 helix: 2.72 (0.34), residues: 236 sheet: 0.73 (1.00), residues: 28 loop : -0.95 (0.71), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 133 HIS 0.002 0.001 HIS A 67 PHE 0.015 0.001 PHE B 31 TYR 0.011 0.002 TYR A 155 ARG 0.004 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.360 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 41 average time/residue: 1.3147 time to fit residues: 55.4931 Evaluate side-chains 33 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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: 0.8484 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3073 Z= 0.196 Angle : 0.513 6.296 4159 Z= 0.272 Chirality : 0.040 0.126 471 Planarity : 0.003 0.029 494 Dihedral : 6.187 43.332 426 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.55 % Allowed : 11.76 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.83 (0.48), residues: 351 helix: 3.05 (0.34), residues: 237 sheet: 0.66 (1.00), residues: 34 loop : -1.45 (0.71), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 133 HIS 0.001 0.000 HIS A 73 PHE 0.014 0.001 PHE B 31 TYR 0.009 0.001 TYR B 158 ARG 0.007 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.370 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 39 average time/residue: 1.4068 time to fit residues: 56.3586 Evaluate side-chains 34 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8468 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3073 Z= 0.164 Angle : 0.499 6.439 4159 Z= 0.265 Chirality : 0.039 0.123 471 Planarity : 0.003 0.029 494 Dihedral : 5.467 33.784 426 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.24 % Allowed : 13.93 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.47), residues: 351 helix: 3.09 (0.34), residues: 239 sheet: 1.24 (1.11), residues: 28 loop : -1.19 (0.67), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 133 HIS 0.003 0.001 HIS B 16 PHE 0.011 0.001 PHE B 31 TYR 0.009 0.001 TYR A 158 ARG 0.006 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.370 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 1.3944 time to fit residues: 54.4682 Evaluate side-chains 35 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3073 Z= 0.286 Angle : 0.568 8.945 4159 Z= 0.294 Chirality : 0.041 0.127 471 Planarity : 0.004 0.033 494 Dihedral : 5.640 32.381 426 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.24 % Allowed : 16.41 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.47), residues: 351 helix: 3.11 (0.33), residues: 236 sheet: 1.04 (1.05), residues: 28 loop : -1.02 (0.68), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 133 HIS 0.002 0.001 HIS B 67 PHE 0.010 0.001 PHE A 181 TYR 0.012 0.002 TYR B 65 ARG 0.006 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.365 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 1.2944 time to fit residues: 51.9699 Evaluate side-chains 35 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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: 0.8466 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3073 Z= 0.155 Angle : 0.517 8.111 4159 Z= 0.266 Chirality : 0.039 0.121 471 Planarity : 0.003 0.030 494 Dihedral : 5.006 26.018 426 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.86 % Allowed : 15.79 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.47), residues: 351 helix: 3.23 (0.33), residues: 238 sheet: 1.27 (1.12), residues: 28 loop : -1.13 (0.66), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 133 HIS 0.001 0.000 HIS A 73 PHE 0.011 0.001 PHE B 31 TYR 0.007 0.001 TYR A 158 ARG 0.011 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.9075 (tp30) cc_final: 0.8718 (tp30) outliers start: 6 outliers final: 5 residues processed: 38 average time/residue: 1.2855 time to fit residues: 50.3043 Evaluate side-chains 37 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.8467 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3073 Z= 0.164 Angle : 0.498 7.737 4159 Z= 0.261 Chirality : 0.038 0.121 471 Planarity : 0.003 0.038 494 Dihedral : 4.812 23.932 426 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.86 % Allowed : 16.41 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.47), residues: 351 helix: 3.26 (0.33), residues: 238 sheet: 1.30 (1.12), residues: 28 loop : -1.14 (0.66), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 133 HIS 0.001 0.000 HIS A 73 PHE 0.010 0.001 PHE B 31 TYR 0.009 0.001 TYR A 158 ARG 0.012 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.9086 (tp30) cc_final: 0.8723 (tp30) outliers start: 6 outliers final: 5 residues processed: 37 average time/residue: 1.2963 time to fit residues: 49.4145 Evaluate side-chains 36 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3073 Z= 0.212 Angle : 0.521 7.452 4159 Z= 0.275 Chirality : 0.039 0.121 471 Planarity : 0.004 0.037 494 Dihedral : 4.925 25.718 426 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.24 % Allowed : 17.34 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.47), residues: 351 helix: 3.25 (0.33), residues: 238 sheet: 1.14 (1.06), residues: 28 loop : -1.05 (0.69), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 133 HIS 0.001 0.000 HIS B 94 PHE 0.008 0.001 PHE B 31 TYR 0.010 0.001 TYR A 158 ARG 0.013 0.001 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.9093 (tp30) cc_final: 0.8719 (tp30) outliers start: 4 outliers final: 4 residues processed: 35 average time/residue: 1.2831 time to fit residues: 46.3048 Evaluate side-chains 35 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8467 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3073 Z= 0.166 Angle : 0.502 7.225 4159 Z= 0.262 Chirality : 0.038 0.119 471 Planarity : 0.003 0.038 494 Dihedral : 4.646 23.805 426 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.55 % Allowed : 17.65 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.47), residues: 351 helix: 3.31 (0.33), residues: 238 sheet: 1.30 (1.12), residues: 28 loop : -1.09 (0.67), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 133 HIS 0.001 0.000 HIS A 73 PHE 0.009 0.001 PHE B 31 TYR 0.008 0.001 TYR A 158 ARG 0.010 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: B 209 GLU cc_start: 0.9081 (tp30) cc_final: 0.8723 (tp30) outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 1.1279 time to fit residues: 42.0276 Evaluate side-chains 34 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.0060 chunk 27 optimal weight: 7.9990 chunk 11 optimal weight: 0.0980 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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: 0.8438 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3073 Z= 0.137 Angle : 0.477 7.120 4159 Z= 0.251 Chirality : 0.038 0.119 471 Planarity : 0.003 0.037 494 Dihedral : 4.194 20.288 426 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.93 % Allowed : 18.27 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.47), residues: 351 helix: 3.37 (0.33), residues: 238 sheet: 1.45 (1.14), residues: 28 loop : -1.06 (0.67), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 133 HIS 0.001 0.000 HIS A 73 PHE 0.007 0.001 PHE B 31 TYR 0.013 0.001 TYR A 152 ARG 0.009 0.000 ARG A 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: B 209 GLU cc_start: 0.9058 (tp30) cc_final: 0.8748 (tp30) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 1.1909 time to fit residues: 47.8621 Evaluate side-chains 34 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.0010 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 overall best weight: 0.7388 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.083857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.059883 restraints weight = 7973.309| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.32 r_work: 0.2873 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3073 Z= 0.152 Angle : 0.501 7.114 4159 Z= 0.257 Chirality : 0.038 0.120 471 Planarity : 0.003 0.032 494 Dihedral : 4.172 20.428 426 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.93 % Allowed : 18.89 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.47), residues: 351 helix: 3.39 (0.33), residues: 238 sheet: 1.46 (1.13), residues: 28 loop : -1.02 (0.67), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 133 HIS 0.001 0.000 HIS A 73 PHE 0.010 0.001 PHE B 31 TYR 0.014 0.001 TYR A 97 ARG 0.009 0.000 ARG A 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1481.66 seconds wall clock time: 26 minutes 57.89 seconds (1617.89 seconds total)