Starting phenix.real_space_refine on Sun Mar 10 15:33:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/03_2024/7yl7_33903_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/03_2024/7yl7_33903.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/03_2024/7yl7_33903_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/03_2024/7yl7_33903_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/03_2024/7yl7_33903_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/03_2024/7yl7_33903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/03_2024/7yl7_33903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/03_2024/7yl7_33903_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/03_2024/7yl7_33903_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1818 2.51 5 N 558 2.21 5 O 600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ARG 11": "NH1" <-> "NH2" Residue "C ARG 11": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "L ARG 11": "NH1" <-> "NH2" Residue "L PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "H ARG 11": "NH1" <-> "NH2" 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: 2988 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "A" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "B" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "K" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 225 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "C" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 225 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "G" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 225 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "L" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 225 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "D" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 225 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "H" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 225 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "J" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "E" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "I" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Time building chain proxies: 1.90, per 1000 atoms: 0.64 Number of scatterers: 2988 At special positions: 0 Unit cell: (144.56, 84.24, 42.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 600 8.00 N 558 7.00 C 1818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS A 2 " - pdb=" SG CYS A 7 " distance=2.03 Simple disulfide: pdb=" SG CYS B 2 " - pdb=" SG CYS B 7 " distance=2.03 Simple disulfide: pdb=" SG CYS J 2 " - pdb=" SG CYS J 7 " distance=2.03 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 7 " distance=2.03 Simple disulfide: pdb=" SG CYS I 2 " - pdb=" SG CYS I 7 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 527.7 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 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: 0.41 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: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 481 1.31 - 1.43: 864 1.43 - 1.56: 1667 1.56 - 1.68: 0 1.68 - 1.81: 12 Bond restraints: 3024 Sorted by residual: bond pdb=" CA THR B 6 " pdb=" C THR B 6 " ideal model delta sigma weight residual 1.532 1.475 0.058 9.60e-03 1.09e+04 3.63e+01 bond pdb=" C THR B 6 " pdb=" N CYS B 7 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.30e-02 5.92e+03 7.20e+00 bond pdb=" CA THR B 6 " pdb=" CB THR B 6 " ideal model delta sigma weight residual 1.533 1.503 0.030 1.37e-02 5.33e+03 4.79e+00 bond pdb=" CA ASN L 14 " pdb=" C ASN L 14 " ideal model delta sigma weight residual 1.520 1.495 0.025 1.21e-02 6.83e+03 4.35e+00 bond pdb=" CA THR F 6 " pdb=" C THR F 6 " ideal model delta sigma weight residual 1.531 1.510 0.021 1.08e-02 8.57e+03 3.86e+00 ... (remaining 3019 not shown) Histogram of bond angle deviations from ideal: 101.62 - 107.57: 63 107.57 - 113.52: 1700 113.52 - 119.47: 655 119.47 - 125.42: 1680 125.42 - 131.38: 12 Bond angle restraints: 4110 Sorted by residual: angle pdb=" C THR B 6 " pdb=" CA THR B 6 " pdb=" CB THR B 6 " ideal model delta sigma weight residual 112.27 101.62 10.65 1.75e+00 3.27e-01 3.70e+01 angle pdb=" C THR B 6 " pdb=" N CYS B 7 " pdb=" CA CYS B 7 " ideal model delta sigma weight residual 123.23 117.31 5.92 1.54e+00 4.22e-01 1.48e+01 angle pdb=" C ALA B 5 " pdb=" N THR B 6 " pdb=" CA THR B 6 " ideal model delta sigma weight residual 122.93 117.56 5.37 1.51e+00 4.39e-01 1.27e+01 angle pdb=" C ASN F 3 " pdb=" N THR F 4 " pdb=" CA THR F 4 " ideal model delta sigma weight residual 122.17 116.80 5.37 1.54e+00 4.22e-01 1.21e+01 angle pdb=" N ASN F 3 " pdb=" CA ASN F 3 " pdb=" C ASN F 3 " ideal model delta sigma weight residual 112.89 117.03 -4.14 1.24e+00 6.50e-01 1.12e+01 ... (remaining 4105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.38: 1505 11.38 - 22.75: 174 22.75 - 34.12: 55 34.12 - 45.50: 18 45.50 - 56.87: 12 Dihedral angle restraints: 1764 sinusoidal: 618 harmonic: 1146 Sorted by residual: dihedral pdb=" CB CYS J 2 " pdb=" SG CYS J 2 " pdb=" SG CYS J 7 " pdb=" CB CYS J 7 " ideal model delta sinusoidal sigma weight residual 93.00 36.13 56.87 1 1.00e+01 1.00e-02 4.35e+01 dihedral pdb=" CB CYS F 2 " pdb=" SG CYS F 2 " pdb=" SG CYS F 7 " pdb=" CB CYS F 7 " ideal model delta sinusoidal sigma weight residual 93.00 37.37 55.63 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS E 2 " pdb=" SG CYS E 2 " pdb=" SG CYS E 7 " pdb=" CB CYS E 7 " ideal model delta sinusoidal sigma weight residual 93.00 38.99 54.01 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 1761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 300 0.026 - 0.052: 114 0.052 - 0.079: 26 0.079 - 0.105: 32 0.105 - 0.131: 26 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA ILE B 26 " pdb=" N ILE B 26 " pdb=" C ILE B 26 " pdb=" CB ILE B 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE I 26 " pdb=" N ILE I 26 " pdb=" C ILE I 26 " pdb=" CB ILE I 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE A 26 " pdb=" N ILE A 26 " pdb=" C ILE A 26 " pdb=" CB ILE A 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 495 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA L 13 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.41e+00 pdb=" C ALA L 13 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA L 13 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN L 14 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 5 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C ALA A 5 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA A 5 " 0.014 2.00e-02 2.50e+03 pdb=" N THR A 6 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 5 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.56e+00 pdb=" C ALA F 5 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA F 5 " 0.014 2.00e-02 2.50e+03 pdb=" N THR F 6 " 0.012 2.00e-02 2.50e+03 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 256 2.74 - 3.28: 2919 3.28 - 3.82: 4596 3.82 - 4.36: 5301 4.36 - 4.90: 10203 Nonbonded interactions: 23275 Sorted by model distance: nonbonded pdb=" OG1 THR B 6 " pdb=" NE ARG K 11 " model vdw 2.196 2.520 nonbonded pdb=" OD1 ASN K 35 " pdb=" OD1 ASN J 35 " model vdw 2.210 3.040 nonbonded pdb=" OD1 ASN G 35 " pdb=" OD1 ASN I 35 " model vdw 2.210 3.040 nonbonded pdb=" O LYS J 1 " pdb=" O CYS I 2 " model vdw 2.243 3.040 nonbonded pdb=" O LYS F 1 " pdb=" O CYS B 2 " model vdw 2.243 3.040 ... (remaining 23270 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 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.010 Extract box with map and model: 3.710 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.350 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 : 0.004 0.058 3024 Z= 0.310 Angle : 1.046 10.649 4110 Z= 0.537 Chirality : 0.044 0.131 498 Planarity : 0.003 0.029 540 Dihedral : 11.947 47.137 990 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -5.16 (0.24), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.18), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 18 PHE 0.009 0.002 PHE J 15 ARG 0.002 0.001 ARG H 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.345 Fit side-chains REVERT: B 11 ARG cc_start: 0.6687 (mtt180) cc_final: 0.5959 (mmm160) REVERT: B 14 ASN cc_start: 0.7951 (m-40) cc_final: 0.7326 (p0) REVERT: H 11 ARG cc_start: 0.4620 (mtt-85) cc_final: 0.4376 (mtp180) REVERT: I 11 ARG cc_start: 0.6767 (mtt180) cc_final: 0.5973 (mmm160) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2293 time to fit residues: 9.3251 Evaluate side-chains 21 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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: 20.0000 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.0020 chunk 32 optimal weight: 0.8980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3024 Z= 0.150 Angle : 0.466 5.333 4110 Z= 0.247 Chirality : 0.042 0.135 498 Planarity : 0.002 0.016 540 Dihedral : 6.516 30.732 438 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.23 % Allowed : 7.72 % Favored : 91.05 % 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: -5.18 (0.23), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.17), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS L 18 PHE 0.006 0.001 PHE K 15 ARG 0.001 0.000 ARG K 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 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: 4 poor density : 21 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: B 11 ARG cc_start: 0.7072 (mtt180) cc_final: 0.6431 (mmp-170) REVERT: I 11 ARG cc_start: 0.6902 (mtt180) cc_final: 0.6139 (mmp-170) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.1518 time to fit residues: 4.7758 Evaluate side-chains 24 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain H residue 34 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 27 optimal weight: 30.0000 chunk 22 optimal weight: 0.0040 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 overall best weight: 3.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 HIS C 18 HIS G 18 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 HIS ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 HIS ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 3024 Z= 0.463 Angle : 0.664 5.704 4110 Z= 0.361 Chirality : 0.048 0.148 498 Planarity : 0.004 0.029 540 Dihedral : 7.979 31.227 438 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 3.40 % Allowed : 12.65 % Favored : 83.95 % 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: -5.02 (0.27), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.21), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 18 PHE 0.019 0.004 PHE G 15 ARG 0.004 0.001 ARG G 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 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: 11 poor density : 22 time to evaluate : 0.312 Fit side-chains REVERT: B 11 ARG cc_start: 0.7122 (mtt180) cc_final: 0.6663 (mmp-170) outliers start: 11 outliers final: 9 residues processed: 27 average time/residue: 0.1696 time to fit residues: 5.7196 Evaluate side-chains 29 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 20 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain I residue 34 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN C 35 ASN G 35 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3024 Z= 0.326 Angle : 0.573 6.858 4110 Z= 0.309 Chirality : 0.046 0.150 498 Planarity : 0.003 0.018 540 Dihedral : 7.324 31.265 438 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 1.85 % Allowed : 19.14 % Favored : 79.01 % 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: -5.14 (0.27), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.20), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 18 PHE 0.013 0.003 PHE G 15 ARG 0.003 0.000 ARG G 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.354 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 25 average time/residue: 0.1698 time to fit residues: 5.3804 Evaluate side-chains 23 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain H residue 26 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3024 Z= 0.239 Angle : 0.514 6.095 4110 Z= 0.273 Chirality : 0.044 0.141 498 Planarity : 0.002 0.012 540 Dihedral : 6.819 31.424 438 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.16 % Allowed : 21.91 % Favored : 75.93 % 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: -5.20 (0.26), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.20), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 18 PHE 0.009 0.002 PHE G 15 ARG 0.002 0.000 ARG G 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 0.345 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 27 average time/residue: 0.1491 time to fit residues: 5.2236 Evaluate side-chains 30 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 23 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.0170 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 3024 Z= 0.365 Angle : 0.589 5.740 4110 Z= 0.317 Chirality : 0.046 0.151 498 Planarity : 0.003 0.019 540 Dihedral : 7.586 31.041 438 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 2.47 % Allowed : 24.07 % Favored : 73.46 % 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: -5.24 (0.27), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.21), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 18 PHE 0.015 0.003 PHE C 15 ARG 0.003 0.000 ARG G 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.300 Fit side-chains REVERT: E 27 LEU cc_start: 0.8483 (tt) cc_final: 0.8040 (mp) REVERT: I 27 LEU cc_start: 0.8432 (tt) cc_final: 0.7956 (mp) outliers start: 8 outliers final: 7 residues processed: 30 average time/residue: 0.2035 time to fit residues: 7.3616 Evaluate side-chains 32 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.0270 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3024 Z= 0.105 Angle : 0.450 5.083 4110 Z= 0.234 Chirality : 0.043 0.136 498 Planarity : 0.001 0.008 540 Dihedral : 6.000 29.608 438 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.93 % Allowed : 24.69 % 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: -5.24 (0.26), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.20), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 18 PHE 0.004 0.001 PHE G 23 ARG 0.001 0.000 ARG K 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 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: 3 poor density : 24 time to evaluate : 0.345 Fit side-chains REVERT: E 27 LEU cc_start: 0.8231 (tt) cc_final: 0.7889 (mp) REVERT: I 27 LEU cc_start: 0.8206 (tt) cc_final: 0.7771 (mp) outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.2082 time to fit residues: 6.0959 Evaluate side-chains 26 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 3024 Z= 0.401 Angle : 0.602 5.127 4110 Z= 0.322 Chirality : 0.046 0.140 498 Planarity : 0.003 0.022 540 Dihedral : 7.532 31.018 438 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.39 % Favored : 86.61 % Rotamer: Outliers : 1.85 % Allowed : 25.62 % 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: -5.21 (0.29), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 18 PHE 0.017 0.003 PHE C 15 ARG 0.003 0.000 ARG G 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 0.401 Fit side-chains REVERT: F 27 LEU cc_start: 0.8342 (tt) cc_final: 0.8054 (mp) REVERT: J 34 SER cc_start: 0.8846 (p) cc_final: 0.8643 (p) REVERT: E 27 LEU cc_start: 0.8460 (tt) cc_final: 0.8032 (mp) REVERT: I 27 LEU cc_start: 0.8540 (tt) cc_final: 0.8061 (mp) outliers start: 6 outliers final: 6 residues processed: 28 average time/residue: 0.1889 time to fit residues: 6.5055 Evaluate side-chains 30 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.0170 chunk 33 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 3024 Z= 0.097 Angle : 0.441 5.250 4110 Z= 0.229 Chirality : 0.043 0.139 498 Planarity : 0.001 0.006 540 Dihedral : 5.955 29.217 438 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.93 % Allowed : 26.23 % 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: -5.19 (0.28), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS J 18 PHE 0.005 0.001 PHE G 23 ARG 0.001 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 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: 3 poor density : 23 time to evaluate : 0.327 Fit side-chains REVERT: E 27 LEU cc_start: 0.8307 (tt) cc_final: 0.7930 (mp) REVERT: I 27 LEU cc_start: 0.8255 (tt) cc_final: 0.7812 (mp) outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.2066 time to fit residues: 5.8160 Evaluate side-chains 25 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 30 optimal weight: 0.0770 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3024 Z= 0.165 Angle : 0.452 4.861 4110 Z= 0.236 Chirality : 0.042 0.138 498 Planarity : 0.001 0.008 540 Dihedral : 6.263 31.284 438 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 1.54 % Allowed : 25.62 % 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: -5.13 (0.29), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 18 PHE 0.006 0.001 PHE C 15 ARG 0.001 0.000 ARG B 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.322 Fit side-chains REVERT: E 27 LEU cc_start: 0.8366 (tt) cc_final: 0.7988 (mp) REVERT: I 27 LEU cc_start: 0.8323 (tt) cc_final: 0.7890 (mp) outliers start: 5 outliers final: 5 residues processed: 25 average time/residue: 0.2225 time to fit residues: 6.7700 Evaluate side-chains 28 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.098625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.076430 restraints weight = 6479.727| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.75 r_work: 0.3609 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 3024 Z= 0.527 Angle : 0.687 5.212 4110 Z= 0.370 Chirality : 0.050 0.155 498 Planarity : 0.005 0.031 540 Dihedral : 8.040 31.348 438 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.94 % Favored : 83.06 % Rotamer: Outliers : 1.85 % Allowed : 25.62 % 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: -5.30 (0.30), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS E 18 PHE 0.022 0.004 PHE C 15 ARG 0.004 0.001 ARG G 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1109.80 seconds wall clock time: 20 minutes 53.87 seconds (1253.87 seconds total)