Starting phenix.real_space_refine on Sun Mar 10 23:14:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrr_11383/03_2024/6zrr_11383_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrr_11383/03_2024/6zrr_11383.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrr_11383/03_2024/6zrr_11383_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrr_11383/03_2024/6zrr_11383_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrr_11383/03_2024/6zrr_11383_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrr_11383/03_2024/6zrr_11383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrr_11383/03_2024/6zrr_11383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrr_11383/03_2024/6zrr_11383_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zrr_11383/03_2024/6zrr_11383_trim_updated.pdb" } resolution = 4.0 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 C 1908 2.51 5 N 540 2.21 5 O 612 1.98 5 H 2664 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5724 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "B" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "C" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "D" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "E" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "F" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "G" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "H" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "I" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "J" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "K" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "L" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "M" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "N" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "O" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "P" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "Q" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "R" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 318 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Time building chain proxies: 2.73, per 1000 atoms: 0.48 Number of scatterers: 5724 At special positions: 0 Unit cell: (61.77, 86.265, 44.73, 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) O 612 8.00 N 540 7.00 C 1908 6.00 H 2664 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.80 Conformation dependent library (CDL) restraints added in 720.4 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 0.96: 913 0.96 - 1.11: 1751 1.11 - 1.25: 486 1.25 - 1.40: 918 1.40 - 1.54: 1710 Bond restraints: 5778 Sorted by residual: bond pdb=" C TYC A 37 " pdb=" NXT TYC A 37 " ideal model delta sigma weight residual 1.451 1.327 0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C TYC P 37 " pdb=" NXT TYC P 37 " ideal model delta sigma weight residual 1.451 1.327 0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C TYC D 37 " pdb=" NXT TYC D 37 " ideal model delta sigma weight residual 1.451 1.327 0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C TYC J 37 " pdb=" NXT TYC J 37 " ideal model delta sigma weight residual 1.451 1.328 0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" C TYC N 37 " pdb=" NXT TYC N 37 " ideal model delta sigma weight residual 1.451 1.328 0.123 2.00e-02 2.50e+03 3.81e+01 ... (remaining 5773 not shown) Histogram of bond angle deviations from ideal: 96.96 - 103.79: 27 103.79 - 110.62: 5291 110.62 - 117.45: 1813 117.45 - 124.28: 2726 124.28 - 131.11: 277 Bond angle restraints: 10134 Sorted by residual: angle pdb=" CG LEU F 16 " pdb=" CB LEU F 16 " pdb=" HB2 LEU F 16 " ideal model delta sigma weight residual 108.00 96.96 11.04 3.00e+00 1.11e-01 1.36e+01 angle pdb=" CG LEU C 16 " pdb=" CB LEU C 16 " pdb=" HB2 LEU C 16 " ideal model delta sigma weight residual 108.00 96.96 11.04 3.00e+00 1.11e-01 1.35e+01 angle pdb=" CG LEU I 16 " pdb=" CB LEU I 16 " pdb=" HB2 LEU I 16 " ideal model delta sigma weight residual 108.00 97.00 11.00 3.00e+00 1.11e-01 1.35e+01 angle pdb=" CG LEU R 16 " pdb=" CB LEU R 16 " pdb=" HB2 LEU R 16 " ideal model delta sigma weight residual 108.00 97.15 10.85 3.00e+00 1.11e-01 1.31e+01 angle pdb=" CG LEU L 16 " pdb=" CB LEU L 16 " pdb=" HB2 LEU L 16 " ideal model delta sigma weight residual 108.00 97.18 10.82 3.00e+00 1.11e-01 1.30e+01 ... (remaining 10129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.72: 2250 13.72 - 27.44: 317 27.44 - 41.16: 67 41.16 - 54.88: 93 54.88 - 68.60: 45 Dihedral angle restraints: 2772 sinusoidal: 1422 harmonic: 1350 Sorted by residual: dihedral pdb=" CA SER D 19 " pdb=" C SER D 19 " pdb=" N GLY D 20 " pdb=" CA GLY D 20 " ideal model delta harmonic sigma weight residual 180.00 154.63 25.37 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA SER H 19 " pdb=" C SER H 19 " pdb=" N GLY H 20 " pdb=" CA GLY H 20 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA SER B 19 " pdb=" C SER B 19 " pdb=" N GLY B 20 " pdb=" CA GLY B 20 " ideal model delta harmonic sigma weight residual 180.00 154.65 25.35 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 2769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 158 0.029 - 0.057: 145 0.057 - 0.086: 116 0.086 - 0.114: 48 0.114 - 0.142: 19 Chirality restraints: 486 Sorted by residual: chirality pdb=" CB ILE O 26 " pdb=" CA ILE O 26 " pdb=" CG1 ILE O 26 " pdb=" CG2 ILE O 26 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CB ILE L 26 " pdb=" CA ILE L 26 " pdb=" CG1 ILE L 26 " pdb=" CG2 ILE L 26 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CB ILE I 26 " pdb=" CA ILE I 26 " pdb=" CG1 ILE I 26 " pdb=" CG2 ILE I 26 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 483 not shown) Planarity restraints: 936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 15 " 0.005 2.00e-02 2.50e+03 7.28e-03 1.59e+00 pdb=" CG PHE I 15 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE I 15 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE I 15 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE I 15 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE I 15 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE I 15 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE I 15 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE I 15 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE I 15 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE I 15 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE I 15 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 15 " 0.005 2.00e-02 2.50e+03 7.24e-03 1.57e+00 pdb=" CG PHE C 15 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE C 15 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 15 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 15 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 15 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 15 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE C 15 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE C 15 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE C 15 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE C 15 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE C 15 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 15 " 0.005 2.00e-02 2.50e+03 7.21e-03 1.56e+00 pdb=" CG PHE O 15 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE O 15 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE O 15 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE O 15 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE O 15 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE O 15 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE O 15 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE O 15 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE O 15 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE O 15 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE O 15 " -0.002 2.00e-02 2.50e+03 ... (remaining 933 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.25: 852 2.25 - 2.81: 12171 2.81 - 3.38: 13273 3.38 - 3.94: 19252 3.94 - 4.50: 26949 Nonbonded interactions: 72497 Sorted by model distance: nonbonded pdb=" HG SER A 28 " pdb=" OH TYC C 37 " model vdw 1.691 1.850 nonbonded pdb=" HG SER D 28 " pdb=" OH TYC F 37 " model vdw 1.708 1.850 nonbonded pdb=" HG SER G 28 " pdb=" OH TYC I 37 " model vdw 1.708 1.850 nonbonded pdb=" HG SER M 28 " pdb=" OH TYC O 37 " model vdw 1.710 1.850 nonbonded pdb=" HG SER J 28 " pdb=" OH TYC L 37 " model vdw 1.722 1.850 ... (remaining 72492 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.090 Extract box with map and model: 5.570 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.540 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 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 : 0.015 0.124 3114 Z= 0.672 Angle : 1.455 11.503 4230 Z= 0.602 Chirality : 0.060 0.142 486 Planarity : 0.004 0.011 558 Dihedral : 14.323 68.602 954 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 28.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: -4.56 (0.31), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.24), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.007 HIS O 18 PHE 0.019 0.005 PHE I 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 35 ASN cc_start: 0.8800 (m-40) cc_final: 0.8588 (m110) REVERT: R 35 ASN cc_start: 0.8122 (m-40) cc_final: 0.7730 (p0) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1420 time to fit residues: 18.4356 Evaluate side-chains 39 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.0770 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3114 Z= 0.122 Angle : 0.578 3.936 4230 Z= 0.305 Chirality : 0.046 0.135 486 Planarity : 0.002 0.013 558 Dihedral : 14.167 78.713 450 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 15.74 % Favored : 84.26 % 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: -4.41 (0.31), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.24), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS P 18 PHE 0.009 0.002 PHE J 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 36 THR cc_start: 0.7744 (t) cc_final: 0.7534 (t) REVERT: O 35 ASN cc_start: 0.8827 (m-40) cc_final: 0.8570 (m110) REVERT: R 35 ASN cc_start: 0.7701 (m-40) cc_final: 0.7343 (p0) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1390 time to fit residues: 12.5557 Evaluate side-chains 38 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN ** Q 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3114 Z= 0.155 Angle : 0.637 6.505 4230 Z= 0.332 Chirality : 0.050 0.136 486 Planarity : 0.002 0.009 558 Dihedral : 12.419 77.138 450 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 1.23 % Allowed : 19.14 % Favored : 79.63 % 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: -4.51 (0.31), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.24), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS P 18 PHE 0.018 0.001 PHE K 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 ASN cc_start: 0.8916 (m-40) cc_final: 0.8563 (m110) REVERT: F 35 ASN cc_start: 0.9147 (m-40) cc_final: 0.8820 (m-40) REVERT: L 35 ASN cc_start: 0.9038 (m-40) cc_final: 0.8779 (m110) REVERT: R 35 ASN cc_start: 0.8261 (m-40) cc_final: 0.7653 (p0) outliers start: 4 outliers final: 2 residues processed: 45 average time/residue: 0.1297 time to fit residues: 8.7715 Evaluate side-chains 34 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain R residue 22 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.0270 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3114 Z= 0.149 Angle : 0.549 3.738 4230 Z= 0.300 Chirality : 0.049 0.140 486 Planarity : 0.002 0.008 558 Dihedral : 11.749 76.868 450 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 26.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 1.85 % Allowed : 19.44 % Favored : 78.70 % 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: -4.45 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS P 18 PHE 0.017 0.002 PHE E 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 ASN cc_start: 0.8924 (m-40) cc_final: 0.8565 (m110) REVERT: F 35 ASN cc_start: 0.9152 (m-40) cc_final: 0.8819 (m-40) REVERT: L 35 ASN cc_start: 0.8999 (m-40) cc_final: 0.8755 (m-40) REVERT: R 35 ASN cc_start: 0.8176 (m-40) cc_final: 0.7654 (p0) outliers start: 6 outliers final: 5 residues processed: 35 average time/residue: 0.1262 time to fit residues: 6.9053 Evaluate side-chains 30 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 21 ASN Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain R residue 22 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 8 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3114 Z= 0.093 Angle : 0.469 3.292 4230 Z= 0.259 Chirality : 0.047 0.125 486 Planarity : 0.002 0.009 558 Dihedral : 11.959 83.506 450 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 1.23 % Allowed : 18.83 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 18 PHE 0.018 0.001 PHE P 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.446 Fit side-chains REVERT: C 26 ILE cc_start: 0.7742 (pt) cc_final: 0.7355 (pt) REVERT: C 35 ASN cc_start: 0.8883 (m-40) cc_final: 0.8556 (m110) REVERT: F 35 ASN cc_start: 0.9155 (m-40) cc_final: 0.8839 (m110) REVERT: J 36 THR cc_start: 0.8788 (t) cc_final: 0.8428 (m) REVERT: L 35 ASN cc_start: 0.9013 (m-40) cc_final: 0.8774 (m-40) REVERT: R 35 ASN cc_start: 0.8102 (m-40) cc_final: 0.7597 (p0) outliers start: 4 outliers final: 1 residues processed: 35 average time/residue: 0.1233 time to fit residues: 6.8679 Evaluate side-chains 25 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3114 Z= 0.194 Angle : 0.636 4.438 4230 Z= 0.338 Chirality : 0.051 0.138 486 Planarity : 0.003 0.012 558 Dihedral : 11.689 79.545 450 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 37.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 1.85 % Allowed : 23.46 % Favored : 74.69 % 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: -4.62 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS P 18 PHE 0.015 0.002 PHE P 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.509 Fit side-chains REVERT: C 35 ASN cc_start: 0.8926 (m-40) cc_final: 0.8503 (m110) REVERT: F 35 ASN cc_start: 0.9186 (m-40) cc_final: 0.8881 (m110) REVERT: R 35 ASN cc_start: 0.8471 (m-40) cc_final: 0.8000 (p0) outliers start: 6 outliers final: 2 residues processed: 32 average time/residue: 0.1235 time to fit residues: 6.3295 Evaluate side-chains 26 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain L residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 0.0000 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.0770 overall best weight: 0.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.6459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3114 Z= 0.089 Angle : 0.460 3.417 4230 Z= 0.258 Chirality : 0.048 0.132 486 Planarity : 0.001 0.007 558 Dihedral : 11.736 78.508 450 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 24.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Rotamer: Outliers : 0.31 % Allowed : 25.31 % Favored : 74.38 % 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: -4.42 (0.36), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS N 18 PHE 0.012 0.001 PHE E 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.507 Fit side-chains REVERT: C 35 ASN cc_start: 0.8867 (m-40) cc_final: 0.8521 (m110) REVERT: F 35 ASN cc_start: 0.9153 (m-40) cc_final: 0.8823 (m110) REVERT: J 36 THR cc_start: 0.8823 (t) cc_final: 0.8514 (m) REVERT: R 35 ASN cc_start: 0.8413 (m-40) cc_final: 0.7924 (p0) outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.1182 time to fit residues: 5.1714 Evaluate side-chains 24 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.0040 chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.6684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3114 Z= 0.099 Angle : 0.470 3.054 4230 Z= 0.261 Chirality : 0.048 0.127 486 Planarity : 0.002 0.007 558 Dihedral : 11.621 78.246 450 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 25.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.11 % Favored : 83.89 % Rotamer: Outliers : 0.31 % Allowed : 26.54 % Favored : 73.15 % 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: -4.40 (0.36), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS E 18 PHE 0.015 0.001 PHE E 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.490 Fit side-chains REVERT: C 35 ASN cc_start: 0.8863 (m-40) cc_final: 0.8465 (m110) REVERT: F 35 ASN cc_start: 0.9107 (m-40) cc_final: 0.8854 (m110) REVERT: R 35 ASN cc_start: 0.8489 (m-40) cc_final: 0.7999 (p0) outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.1203 time to fit residues: 4.9826 Evaluate side-chains 26 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.6866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3114 Z= 0.111 Angle : 0.490 3.058 4230 Z= 0.272 Chirality : 0.048 0.126 486 Planarity : 0.002 0.008 558 Dihedral : 11.591 77.959 450 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 27.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % Rotamer: Outliers : 0.62 % Allowed : 26.23 % Favored : 73.15 % 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: -4.44 (0.36), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS E 18 PHE 0.015 0.002 PHE E 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.458 Fit side-chains REVERT: C 35 ASN cc_start: 0.8860 (m-40) cc_final: 0.8476 (m110) REVERT: F 35 ASN cc_start: 0.9114 (m-40) cc_final: 0.8864 (m110) REVERT: R 35 ASN cc_start: 0.8762 (m-40) cc_final: 0.8116 (p0) outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.1229 time to fit residues: 5.1694 Evaluate side-chains 25 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3114 Z= 0.150 Angle : 0.555 4.062 4230 Z= 0.301 Chirality : 0.050 0.128 486 Planarity : 0.003 0.010 558 Dihedral : 11.490 77.174 450 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 31.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.44 % Favored : 80.56 % Rotamer: Outliers : 0.31 % Allowed : 26.85 % Favored : 72.84 % 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: -4.64 (0.36), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS P 18 PHE 0.016 0.002 PHE E 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.515 Fit side-chains REVERT: C 35 ASN cc_start: 0.8893 (m-40) cc_final: 0.8491 (m110) REVERT: F 35 ASN cc_start: 0.9142 (m-40) cc_final: 0.8912 (m110) REVERT: R 35 ASN cc_start: 0.8790 (m-40) cc_final: 0.8181 (p0) outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.1223 time to fit residues: 4.8877 Evaluate side-chains 25 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.223033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.5185 r_free = 0.5185 target = 0.141819 restraints weight = 16116.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5212 r_free = 0.5212 target = 0.144051 restraints weight = 10556.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5241 r_free = 0.5241 target = 0.145904 restraints weight = 7679.680| |-----------------------------------------------------------------------------| r_work (final): 0.4628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.7147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3114 Z= 0.143 Angle : 0.543 3.329 4230 Z= 0.300 Chirality : 0.050 0.149 486 Planarity : 0.002 0.010 558 Dihedral : 11.437 77.965 450 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 31.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.39 % Favored : 83.61 % Rotamer: Outliers : 0.62 % Allowed : 26.85 % Favored : 72.53 % 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: -4.75 (0.36), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS N 18 PHE 0.015 0.002 PHE E 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2410.40 seconds wall clock time: 42 minutes 59.31 seconds (2579.31 seconds total)