Starting phenix.real_space_refine on Tue Feb 13 21:13:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1o_11031/02_2024/6z1o_11031.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1o_11031/02_2024/6z1o_11031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1o_11031/02_2024/6z1o_11031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1o_11031/02_2024/6z1o_11031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1o_11031/02_2024/6z1o_11031.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1o_11031/02_2024/6z1o_11031.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 S 12 5.16 5 C 2436 2.51 5 N 714 2.21 5 O 810 1.98 5 H 3786 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 25": "OD1" <-> "OD2" Residue "D TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D ASP 84": "OD1" <-> "OD2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F ASP 84": "OD1" <-> "OD2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 25": "OD1" <-> "OD2" Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 7758 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1293 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain breaks: 1 Chain: "E" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1293 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain breaks: 1 Chain: "F" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1293 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain breaks: 1 Chain: "C" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1293 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain breaks: 1 Chain: "B" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1293 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain breaks: 1 Chain: "A" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1293 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain breaks: 1 Time building chain proxies: 3.94, per 1000 atoms: 0.51 Number of scatterers: 7758 At special positions: 0 Unit cell: (83.2, 82.16, 46.8, 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 12 16.00 O 810 8.00 N 714 7.00 C 2436 6.00 H 3786 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=1.99 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=1.99 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=1.99 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=1.99 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=1.99 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 87 " distance=1.99 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.46 Conformation dependent library (CDL) restraints added in 740.6 milliseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 43.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 23 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA4, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA5, first strand: chain 'A' and resid 34 through 37 Processing sheet with id=AA6, first strand: chain 'A' and resid 43 through 47 Processing sheet with id=AA7, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA8, first strand: chain 'A' and resid 64 through 65 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 64 through 65 current: chain 'B' and resid 64 through 65 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 64 through 65 current: chain 'C' and resid 64 through 65 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 64 through 65 current: chain 'D' and resid 64 through 65 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 64 through 65 current: chain 'E' and resid 64 through 65 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 64 through 65 current: chain 'F' and resid 64 through 65 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AB1, first strand: chain 'A' and resid 79 through 82 Processing sheet with id=AB2, first strand: chain 'A' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 85 through 86 current: chain 'B' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 85 through 86 current: chain 'C' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 85 through 86 current: chain 'D' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 85 through 86 current: chain 'E' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 85 through 86 current: chain 'F' and resid 85 through 86 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 88 through 91 Processing sheet with id=AB4, first strand: chain 'A' and resid 95 through 97 Processing sheet with id=AB5, first strand: chain 'A' and resid 103 through 106 185 hydrogen bonds defined for protein. 555 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: 2.73 Time building geometry restraints manager: 5.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3786 1.03 - 1.23: 133 1.23 - 1.42: 1637 1.42 - 1.61: 2250 1.61 - 1.81: 12 Bond restraints: 7818 Sorted by residual: bond pdb=" CA ALA D 94 " pdb=" CB ALA D 94 " ideal model delta sigma weight residual 1.530 1.472 0.058 1.24e-02 6.50e+03 2.15e+01 bond pdb=" CA ALA F 94 " pdb=" CB ALA F 94 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.24e-02 6.50e+03 2.13e+01 bond pdb=" CA ALA E 94 " pdb=" CB ALA E 94 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.24e-02 6.50e+03 2.11e+01 bond pdb=" CA ALA C 94 " pdb=" CB ALA C 94 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.24e-02 6.50e+03 2.09e+01 bond pdb=" CA ALA B 94 " pdb=" CB ALA B 94 " ideal model delta sigma weight residual 1.530 1.474 0.056 1.24e-02 6.50e+03 2.06e+01 ... (remaining 7813 not shown) Histogram of bond angle deviations from ideal: 100.74 - 107.35: 593 107.35 - 113.97: 8586 113.97 - 120.59: 2720 120.59 - 127.21: 1973 127.21 - 133.82: 66 Bond angle restraints: 13938 Sorted by residual: angle pdb=" C PRO B 39 " pdb=" CA PRO B 39 " pdb=" CB PRO B 39 " ideal model delta sigma weight residual 111.11 103.02 8.09 1.17e+00 7.31e-01 4.78e+01 angle pdb=" C PRO F 39 " pdb=" CA PRO F 39 " pdb=" CB PRO F 39 " ideal model delta sigma weight residual 111.11 103.03 8.08 1.17e+00 7.31e-01 4.77e+01 angle pdb=" C PRO A 39 " pdb=" CA PRO A 39 " pdb=" CB PRO A 39 " ideal model delta sigma weight residual 111.11 103.05 8.06 1.17e+00 7.31e-01 4.74e+01 angle pdb=" C PRO C 39 " pdb=" CA PRO C 39 " pdb=" CB PRO C 39 " ideal model delta sigma weight residual 111.11 103.06 8.05 1.17e+00 7.31e-01 4.73e+01 angle pdb=" C PRO E 39 " pdb=" CA PRO E 39 " pdb=" CB PRO E 39 " ideal model delta sigma weight residual 111.11 103.08 8.03 1.17e+00 7.31e-01 4.71e+01 ... (remaining 13933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 3342 17.52 - 35.04: 300 35.04 - 52.56: 96 52.56 - 70.07: 6 70.07 - 87.59: 6 Dihedral angle restraints: 3750 sinusoidal: 2004 harmonic: 1746 Sorted by residual: dihedral pdb=" C CYS F 87 " pdb=" N CYS F 87 " pdb=" CA CYS F 87 " pdb=" CB CYS F 87 " ideal model delta harmonic sigma weight residual -122.60 -132.10 9.50 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" C CYS C 87 " pdb=" N CYS C 87 " pdb=" CA CYS C 87 " pdb=" CB CYS C 87 " ideal model delta harmonic sigma weight residual -122.60 -132.04 9.44 0 2.50e+00 1.60e-01 1.43e+01 dihedral pdb=" C CYS D 87 " pdb=" N CYS D 87 " pdb=" CA CYS D 87 " pdb=" CB CYS D 87 " ideal model delta harmonic sigma weight residual -122.60 -132.04 9.44 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 3747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 222 0.072 - 0.144: 224 0.144 - 0.216: 122 0.216 - 0.289: 26 0.289 - 0.361: 18 Chirality restraints: 612 Sorted by residual: chirality pdb=" CA CYS F 87 " pdb=" N CYS F 87 " pdb=" C CYS F 87 " pdb=" CB CYS F 87 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA CYS A 87 " pdb=" N CYS A 87 " pdb=" C CYS A 87 " pdb=" CB CYS A 87 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CA CYS B 87 " pdb=" N CYS B 87 " pdb=" C CYS B 87 " pdb=" CB CYS B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 609 not shown) Planarity restraints: 1224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 95 " 0.222 2.00e-02 2.50e+03 2.76e-01 1.14e+03 pdb=" CG ASN C 95 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN C 95 " -0.223 2.00e-02 2.50e+03 pdb=" ND2 ASN C 95 " 0.010 2.00e-02 2.50e+03 pdb="HD21 ASN C 95 " -0.421 2.00e-02 2.50e+03 pdb="HD22 ASN C 95 " 0.425 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 95 " 0.221 2.00e-02 2.50e+03 2.76e-01 1.14e+03 pdb=" CG ASN A 95 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 95 " -0.222 2.00e-02 2.50e+03 pdb=" ND2 ASN A 95 " 0.010 2.00e-02 2.50e+03 pdb="HD21 ASN A 95 " -0.421 2.00e-02 2.50e+03 pdb="HD22 ASN A 95 " 0.425 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 95 " 0.221 2.00e-02 2.50e+03 2.76e-01 1.14e+03 pdb=" CG ASN D 95 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN D 95 " -0.222 2.00e-02 2.50e+03 pdb=" ND2 ASN D 95 " 0.010 2.00e-02 2.50e+03 pdb="HD21 ASN D 95 " -0.421 2.00e-02 2.50e+03 pdb="HD22 ASN D 95 " 0.425 2.00e-02 2.50e+03 ... (remaining 1221 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 675 2.22 - 2.82: 16052 2.82 - 3.41: 18599 3.41 - 4.01: 29086 4.01 - 4.60: 40908 Nonbonded interactions: 105320 Sorted by model distance: nonbonded pdb=" OD1 ASN B 68 " pdb=" HG SER B 71 " model vdw 1.628 1.850 nonbonded pdb=" OD1 ASN C 68 " pdb=" HG SER C 71 " model vdw 1.628 1.850 nonbonded pdb=" OD1 ASN D 68 " pdb=" HG SER D 71 " model vdw 1.628 1.850 nonbonded pdb=" OD1 ASN E 68 " pdb=" HG SER E 71 " model vdw 1.629 1.850 nonbonded pdb=" OD1 ASN F 68 " pdb=" HG SER F 71 " model vdw 1.629 1.850 ... (remaining 105315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.120 Extract box with map and model: 5.890 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 27.160 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 : 0.013 0.058 4032 Z= 0.891 Angle : 2.231 9.468 5454 Z= 1.581 Chirality : 0.128 0.361 612 Planarity : 0.013 0.047 714 Dihedral : 13.750 52.333 1404 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % 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: -4.26 (0.25), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.19), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.007 TRP E 34 HIS 0.008 0.005 HIS D 96 PHE 0.018 0.005 PHE A 99 TYR 0.027 0.006 TYR A 86 ARG 0.002 0.001 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 80 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7385 (mt-10) REVERT: E 48 PHE cc_start: 0.8219 (m-80) cc_final: 0.7779 (m-80) REVERT: E 104 LYS cc_start: 0.7713 (tttt) cc_final: 0.7414 (ttmt) REVERT: F 84 ASP cc_start: 0.8206 (t0) cc_final: 0.7766 (t0) REVERT: C 48 PHE cc_start: 0.8223 (m-80) cc_final: 0.7935 (m-80) REVERT: C 82 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7602 (mt-10) REVERT: B 48 PHE cc_start: 0.8442 (m-80) cc_final: 0.8135 (m-80) REVERT: A 19 ARG cc_start: 0.7976 (ttt180) cc_final: 0.7148 (mmp-170) REVERT: A 34 TRP cc_start: 0.7391 (t-100) cc_final: 0.6958 (t60) REVERT: A 80 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6766 (mt-10) REVERT: A 104 LYS cc_start: 0.7866 (tttt) cc_final: 0.7452 (tttt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.4508 time to fit residues: 85.1238 Evaluate side-chains 99 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN D 68 ASN C 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4032 Z= 0.221 Angle : 0.635 4.446 5454 Z= 0.349 Chirality : 0.046 0.136 612 Planarity : 0.005 0.043 714 Dihedral : 6.343 18.596 576 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.76 % Allowed : 13.85 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 34 HIS 0.002 0.001 HIS F 96 PHE 0.008 0.001 PHE F 99 TYR 0.016 0.002 TYR F 85 ARG 0.004 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 LYS cc_start: 0.7615 (tttt) cc_final: 0.7236 (tmtt) REVERT: B 48 PHE cc_start: 0.8427 (m-80) cc_final: 0.8219 (m-80) REVERT: B 97 GLN cc_start: 0.8791 (mp10) cc_final: 0.8405 (mt0) REVERT: A 19 ARG cc_start: 0.8152 (ttt180) cc_final: 0.7406 (mmp-170) REVERT: A 23 GLN cc_start: 0.7946 (tt0) cc_final: 0.7662 (tt0) REVERT: A 34 TRP cc_start: 0.7981 (t-100) cc_final: 0.7027 (t60) REVERT: A 104 LYS cc_start: 0.7694 (tttt) cc_final: 0.7187 (tttm) outliers start: 16 outliers final: 9 residues processed: 100 average time/residue: 0.3488 time to fit residues: 44.6619 Evaluate side-chains 83 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4032 Z= 0.339 Angle : 0.651 4.797 5454 Z= 0.362 Chirality : 0.046 0.130 612 Planarity : 0.005 0.037 714 Dihedral : 6.229 20.804 576 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.46 % Allowed : 15.26 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 34 HIS 0.002 0.001 HIS A 96 PHE 0.010 0.001 PHE F 99 TYR 0.019 0.002 TYR F 85 ARG 0.009 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 68 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 48 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7888 (t80) REVERT: C 48 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7613 (t80) REVERT: C 80 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7527 (mt-10) REVERT: B 48 PHE cc_start: 0.8538 (m-80) cc_final: 0.8332 (m-80) REVERT: B 84 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.7967 (t0) REVERT: B 97 GLN cc_start: 0.8932 (mp10) cc_final: 0.8649 (mt0) outliers start: 19 outliers final: 13 residues processed: 79 average time/residue: 0.2800 time to fit residues: 28.5377 Evaluate side-chains 75 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4032 Z= 0.240 Angle : 0.569 4.496 5454 Z= 0.313 Chirality : 0.044 0.134 612 Planarity : 0.004 0.036 714 Dihedral : 5.951 17.605 576 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.16 % Allowed : 16.43 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 34 HIS 0.002 0.001 HIS F 96 PHE 0.003 0.001 PHE B 61 TYR 0.011 0.001 TYR F 85 ARG 0.003 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 64 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: D 48 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7875 (t80) REVERT: E 104 LYS cc_start: 0.7670 (tttt) cc_final: 0.7263 (tmtt) REVERT: C 48 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7626 (t80) REVERT: B 97 GLN cc_start: 0.8917 (mp10) cc_final: 0.8647 (mt0) outliers start: 22 outliers final: 17 residues processed: 74 average time/residue: 0.2591 time to fit residues: 25.5567 Evaluate side-chains 79 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 34 TRP Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4032 Z= 0.252 Angle : 0.565 4.578 5454 Z= 0.309 Chirality : 0.044 0.129 612 Planarity : 0.004 0.034 714 Dihedral : 5.829 18.231 576 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.63 % Allowed : 16.20 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 34 HIS 0.002 0.001 HIS F 96 PHE 0.004 0.001 PHE B 61 TYR 0.011 0.001 TYR F 85 ARG 0.003 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 62 time to evaluate : 0.698 Fit side-chains REVERT: E 104 LYS cc_start: 0.7674 (tttt) cc_final: 0.7274 (tmtt) REVERT: C 48 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7656 (t80) REVERT: B 97 GLN cc_start: 0.8936 (mp10) cc_final: 0.8674 (mt0) outliers start: 24 outliers final: 22 residues processed: 73 average time/residue: 0.2498 time to fit residues: 24.2401 Evaluate side-chains 82 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 59 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 34 TRP Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.6703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4032 Z= 0.260 Angle : 0.562 4.568 5454 Z= 0.309 Chirality : 0.044 0.130 612 Planarity : 0.003 0.034 714 Dihedral : 5.801 17.880 576 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 5.87 % Allowed : 15.73 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.22), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 34 HIS 0.003 0.001 HIS F 96 PHE 0.003 0.001 PHE B 61 TYR 0.010 0.001 TYR F 85 ARG 0.002 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 63 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: E 80 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7955 (mm-30) REVERT: E 104 LYS cc_start: 0.7686 (tttt) cc_final: 0.7268 (tmtt) REVERT: C 48 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7669 (t80) REVERT: B 85 TYR cc_start: 0.8306 (t80) cc_final: 0.8030 (t80) REVERT: A 90 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.6931 (tpm170) outliers start: 25 outliers final: 21 residues processed: 76 average time/residue: 0.3302 time to fit residues: 31.2987 Evaluate side-chains 83 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 60 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 TRP Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.6872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4032 Z= 0.316 Angle : 0.597 4.700 5454 Z= 0.326 Chirality : 0.044 0.127 612 Planarity : 0.003 0.033 714 Dihedral : 5.885 18.236 576 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 6.34 % Allowed : 15.26 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.22), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 34 HIS 0.002 0.001 HIS F 96 PHE 0.004 0.001 PHE B 61 TYR 0.013 0.002 TYR F 85 ARG 0.002 0.001 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 62 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 80 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7863 (mm-30) REVERT: E 104 LYS cc_start: 0.7739 (tttt) cc_final: 0.7299 (tmtt) REVERT: C 48 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7718 (t80) REVERT: A 90 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.6962 (tpm170) outliers start: 27 outliers final: 24 residues processed: 75 average time/residue: 0.3317 time to fit residues: 31.9477 Evaluate side-chains 86 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 60 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 34 TRP Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.6995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4032 Z= 0.282 Angle : 0.574 4.599 5454 Z= 0.314 Chirality : 0.044 0.127 612 Planarity : 0.003 0.032 714 Dihedral : 5.833 18.009 576 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 6.57 % Allowed : 14.79 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.22), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 34 HIS 0.003 0.001 HIS F 96 PHE 0.004 0.001 PHE B 61 TYR 0.011 0.001 TYR F 85 ARG 0.002 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 61 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 104 LYS cc_start: 0.7733 (tttt) cc_final: 0.7295 (tmtt) REVERT: C 48 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7725 (t80) REVERT: A 90 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.6965 (tpm170) outliers start: 28 outliers final: 22 residues processed: 75 average time/residue: 0.3290 time to fit residues: 31.6738 Evaluate side-chains 84 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 60 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 TRP Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.7095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4032 Z= 0.241 Angle : 0.558 4.543 5454 Z= 0.304 Chirality : 0.044 0.125 612 Planarity : 0.003 0.031 714 Dihedral : 5.738 17.710 576 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.87 % Allowed : 15.96 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.22), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 34 HIS 0.002 0.001 HIS D 96 PHE 0.003 0.001 PHE B 61 TYR 0.011 0.001 TYR F 85 ARG 0.002 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 66 time to evaluate : 0.725 Fit side-chains REVERT: E 80 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7847 (mm-30) REVERT: E 104 LYS cc_start: 0.7713 (tttt) cc_final: 0.7281 (tmtt) REVERT: C 48 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7710 (t80) REVERT: B 85 TYR cc_start: 0.8229 (t80) cc_final: 0.7934 (t80) REVERT: A 90 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.6957 (tpm170) outliers start: 25 outliers final: 20 residues processed: 77 average time/residue: 0.2958 time to fit residues: 29.5202 Evaluate side-chains 86 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 64 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 TRP Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.7181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4032 Z= 0.224 Angle : 0.555 5.057 5454 Z= 0.302 Chirality : 0.044 0.151 612 Planarity : 0.003 0.031 714 Dihedral : 5.675 17.122 576 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 5.40 % Allowed : 17.14 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.22), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 34 HIS 0.003 0.001 HIS D 96 PHE 0.003 0.001 PHE B 61 TYR 0.010 0.001 TYR F 85 ARG 0.002 0.000 ARG A 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 0.684 Fit side-chains REVERT: E 80 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7672 (mm-30) REVERT: E 104 LYS cc_start: 0.7715 (tttt) cc_final: 0.7286 (tmtt) REVERT: C 48 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7680 (t80) REVERT: B 85 TYR cc_start: 0.8197 (t80) cc_final: 0.7907 (t80) outliers start: 23 outliers final: 22 residues processed: 72 average time/residue: 0.2330 time to fit residues: 23.0957 Evaluate side-chains 85 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 62 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 TRP Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain A residue 34 TRP Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.117059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.110524 restraints weight = 20366.769| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.85 r_work: 0.3692 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.7234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4032 Z= 0.245 Angle : 0.565 4.900 5454 Z= 0.307 Chirality : 0.044 0.146 612 Planarity : 0.003 0.031 714 Dihedral : 5.681 17.120 576 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 5.87 % Allowed : 17.14 % Favored : 77.00 % 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: -3.38 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.22), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 34 HIS 0.003 0.001 HIS D 96 PHE 0.003 0.001 PHE B 61 TYR 0.011 0.001 TYR F 85 ARG 0.002 0.000 ARG C 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3100.20 seconds wall clock time: 55 minutes 23.85 seconds (3323.85 seconds total)