Starting phenix.real_space_refine (version: dev) on Fri Feb 17 01:20:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/02_2023/7yl7_33903_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/02_2023/7yl7_33903.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/02_2023/7yl7_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_33903/02_2023/7yl7_33903_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/02_2023/7yl7_33903_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/02_2023/7yl7_33903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/02_2023/7yl7_33903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/02_2023/7yl7_33903_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl7_33903/02_2023/7yl7_33903_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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-4877/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: 2.01, per 1000 atoms: 0.67 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: 1.29 Conformation dependent library (CDL) restraints added in 449.9 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: 0.13 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: 1.36 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: 1499 11.38 - 22.75: 168 22.75 - 34.12: 43 34.12 - 45.50: 18 45.50 - 56.87: 12 Dihedral angle restraints: 1740 sinusoidal: 594 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 1737 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 3.860 Check model and map are aligned: 0.050 Process input model: 12.150 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 11.576 47.137 966 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 % 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 *********************** 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 : 0.377 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2418 time to fit residues: 9.8139 Evaluate side-chains 21 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4662 ------------------------------------------------------------------------------- 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 14 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN C 35 ASN G 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 3024 Z= 0.145 Angle : 0.469 5.318 4110 Z= 0.248 Chirality : 0.043 0.130 498 Planarity : 0.002 0.017 540 Dihedral : 4.744 17.237 414 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 1.54 % 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 (0.23), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.17), residues: 366 *********************** 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 23 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 0.323 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 22 average time/residue: 0.1067 time to fit residues: 3.3351 Evaluate side-chains 21 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 17 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0283 time to fit residues: 0.5979 ------------------------------------------------------------------------------- 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: 0.9980 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 G 18 HIS L 18 HIS ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 3024 Z= 0.358 Angle : 0.579 5.065 4110 Z= 0.316 Chirality : 0.045 0.147 498 Planarity : 0.003 0.022 540 Dihedral : 6.262 26.814 414 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer Outliers : 1.85 % 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: -5.11 (0.26), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.20), residues: 366 *********************** 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 29 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.353 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 24 average time/residue: 0.1327 time to fit residues: 4.2845 Evaluate side-chains 23 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0309 time to fit residues: 0.6459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** C 18 HIS C 35 ASN D 18 HIS ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.058 3024 Z= 0.484 Angle : 0.671 5.532 4110 Z= 0.366 Chirality : 0.049 0.149 498 Planarity : 0.004 0.026 540 Dihedral : 6.969 27.769 414 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer Outliers : 0.93 % 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: -5.19 (0.27), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.20), residues: 366 *********************** 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 27 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.326 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 27 average time/residue: 0.1671 time to fit residues: 5.7948 Evaluate side-chains 23 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0335 time to fit residues: 0.6479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 3024 Z= 0.162 Angle : 0.467 4.160 4110 Z= 0.251 Chirality : 0.043 0.140 498 Planarity : 0.001 0.008 540 Dihedral : 5.172 19.106 414 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer Outliers : 0.93 % 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: -5.23 (0.26), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.20), residues: 366 *********************** 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 23 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.358 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 20 average time/residue: 0.1982 time to fit residues: 4.9995 Evaluate side-chains 22 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0388 time to fit residues: 0.5806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 3024 Z= 0.288 Angle : 0.520 4.402 4110 Z= 0.281 Chirality : 0.044 0.144 498 Planarity : 0.002 0.014 540 Dihedral : 5.949 24.485 414 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer Outliers : 0.93 % 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: -5.18 (0.27), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.21), residues: 366 *********************** 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 27 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.486 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.2408 time to fit residues: 7.6578 Evaluate side-chains 24 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0303 time to fit residues: 0.5402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.0060 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- 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 ** 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: 0.7826 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 3024 Z= 0.159 Angle : 0.462 5.370 4110 Z= 0.243 Chirality : 0.043 0.139 498 Planarity : 0.001 0.008 540 Dihedral : 5.050 19.753 414 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.93 % 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: -5.18 (0.27), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.21), residues: 366 *********************** 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 26 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.368 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.1778 time to fit residues: 5.2290 Evaluate side-chains 23 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0303 time to fit residues: 0.5338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 33 optimal weight: 0.2980 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 25 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 ** 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: 0.7814 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 3024 Z= 0.150 Angle : 0.445 5.103 4110 Z= 0.233 Chirality : 0.042 0.138 498 Planarity : 0.001 0.007 540 Dihedral : 4.778 19.176 414 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 0.31 % 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: -5.12 (0.28), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.21), residues: 366 *********************** 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 23 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.382 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.1907 time to fit residues: 5.3376 Evaluate side-chains 22 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.340 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 34 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** J 10 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3024 Z= 0.198 Angle : 0.467 7.140 4110 Z= 0.243 Chirality : 0.043 0.139 498 Planarity : 0.002 0.010 540 Dihedral : 5.073 20.668 414 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer Outliers : 0.31 % 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: -5.11 (0.28), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.21), residues: 366 *********************** 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 24 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.436 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 23 average time/residue: 0.2067 time to fit residues: 5.7607 Evaluate side-chains 24 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.322 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0298 time to fit residues: 0.4565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 0.0030 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** J 10 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.016 3024 Z= 0.123 Angle : 0.438 7.320 4110 Z= 0.223 Chirality : 0.042 0.135 498 Planarity : 0.001 0.006 540 Dihedral : 4.442 18.052 414 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.10 (0.28), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.21), residues: 366 ********************** 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 21 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.329 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1958 time to fit residues: 5.2168 Evaluate side-chains 20 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 0.0670 overall best weight: 2.3724 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** J 31 ASN I 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.101568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.079108 restraints weight = 6294.897| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.81 r_work: 0.3649 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4000 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= 0.361 Angle : 0.565 7.821 4110 Z= 0.299 Chirality : 0.046 0.142 498 Planarity : 0.003 0.020 540 Dihedral : 5.932 26.235 414 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer Outliers : 0.31 % 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: -5.07 (0.29), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.22), residues: 366 =============================================================================== Job complete usr+sys time: 1107.84 seconds wall clock time: 20 minutes 50.51 seconds (1250.51 seconds total)