Starting phenix.real_space_refine on Sun Mar 10 15:30:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl3_33902/03_2024/7yl3_33902_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl3_33902/03_2024/7yl3_33902.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl3_33902/03_2024/7yl3_33902_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl3_33902/03_2024/7yl3_33902_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl3_33902/03_2024/7yl3_33902_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl3_33902/03_2024/7yl3_33902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl3_33902/03_2024/7yl3_33902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl3_33902/03_2024/7yl3_33902_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yl3_33902/03_2024/7yl3_33902_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 1800 2.51 5 N 552 2.21 5 O 594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 11": "NH1" <-> "NH2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 11": "NH1" <-> "NH2" Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 11": "NH1" <-> "NH2" Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 11": "NH1" <-> "NH2" Residue "J PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 11": "NH1" <-> "NH2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 11": "NH1" <-> "NH2" Residue "L PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 2958 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" 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: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "I" 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: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} 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: "F" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} 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: "H" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} 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: "G" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "L" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "D" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Time building chain proxies: 2.16, per 1000 atoms: 0.73 Number of scatterers: 2958 At special positions: 0 Unit cell: (132.08, 88.4, 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 594 8.00 N 552 7.00 C 1800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS C 2 " - pdb=" SG CYS C 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 2 " - pdb=" SG CYS B 7 " distance=2.85 Simple disulfide: pdb=" SG CYS I 2 " - pdb=" SG CYS I 7 " distance=2.03 Simple disulfide: pdb=" SG CYS A 2 " - pdb=" SG CYS A 7 " distance=2.03 Simple disulfide: pdb=" SG CYS J 2 " - pdb=" SG CYS J 7 " distance=2.03 Simple disulfide: pdb=" SG CYS B 2 " - pdb=" SG CYS B 7 " distance=2.03 Simple disulfide: pdb=" SG CYS L 2 " - pdb=" SG CYS L 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: 1.14 Conformation dependent library (CDL) restraints added in 562.1 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 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: 0.46 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: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 521 1.33 - 1.45: 871 1.45 - 1.57: 1590 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 2994 Sorted by residual: bond pdb=" C THR E 36 " pdb=" N TYC E 37 " ideal model delta sigma weight residual 1.329 1.204 0.125 1.40e-02 5.10e+03 7.95e+01 bond pdb=" C THR F 36 " pdb=" N TYC F 37 " ideal model delta sigma weight residual 1.329 1.205 0.124 1.40e-02 5.10e+03 7.91e+01 bond pdb=" C THR G 36 " pdb=" N TYC G 37 " ideal model delta sigma weight residual 1.329 1.205 0.124 1.40e-02 5.10e+03 7.91e+01 bond pdb=" C THR K 36 " pdb=" N TYC K 37 " ideal model delta sigma weight residual 1.329 1.207 0.122 1.40e-02 5.10e+03 7.63e+01 bond pdb=" C THR H 36 " pdb=" N TYC H 37 " ideal model delta sigma weight residual 1.329 1.207 0.122 1.40e-02 5.10e+03 7.55e+01 ... (remaining 2989 not shown) Histogram of bond angle deviations from ideal: 102.94 - 112.62: 1671 112.62 - 122.30: 1733 122.30 - 131.99: 646 131.99 - 141.67: 6 141.67 - 151.35: 12 Bond angle restraints: 4068 Sorted by residual: angle pdb=" C THR E 36 " pdb=" N TYC E 37 " pdb=" CA TYC E 37 " ideal model delta sigma weight residual 121.70 151.35 -29.65 1.80e+00 3.09e-01 2.71e+02 angle pdb=" C THR G 36 " pdb=" N TYC G 37 " pdb=" CA TYC G 37 " ideal model delta sigma weight residual 121.70 151.34 -29.64 1.80e+00 3.09e-01 2.71e+02 angle pdb=" C THR F 36 " pdb=" N TYC F 37 " pdb=" CA TYC F 37 " ideal model delta sigma weight residual 121.70 151.34 -29.64 1.80e+00 3.09e-01 2.71e+02 angle pdb=" C THR D 36 " pdb=" N TYC D 37 " pdb=" CA TYC D 37 " ideal model delta sigma weight residual 121.70 150.02 -28.32 1.80e+00 3.09e-01 2.48e+02 angle pdb=" C THR K 36 " pdb=" N TYC K 37 " pdb=" CA TYC K 37 " ideal model delta sigma weight residual 121.70 150.00 -28.30 1.80e+00 3.09e-01 2.47e+02 ... (remaining 4063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.30: 1482 10.30 - 20.60: 172 20.60 - 30.90: 47 30.90 - 41.21: 24 41.21 - 51.51: 24 Dihedral angle restraints: 1749 sinusoidal: 621 harmonic: 1128 Sorted by residual: dihedral pdb=" CB CYS C 2 " pdb=" SG CYS C 2 " pdb=" SG CYS B 7 " pdb=" CB CYS B 7 " ideal model delta sinusoidal sigma weight residual 93.00 64.33 28.67 1 1.00e+01 1.00e-02 1.18e+01 dihedral pdb=" CA CYS I 2 " pdb=" CB CYS I 2 " pdb=" SG CYS I 2 " pdb=" SG CYS I 7 " ideal model delta sinusoidal sigma weight residual -73.00 -123.92 50.92 1 2.00e+01 2.50e-03 8.87e+00 dihedral pdb=" CA CYS B 2 " pdb=" CB CYS B 2 " pdb=" SG CYS B 2 " pdb=" SG CYS B 7 " ideal model delta sinusoidal sigma weight residual -73.00 -123.91 50.91 1 2.00e+01 2.50e-03 8.87e+00 ... (remaining 1746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 408 0.058 - 0.117: 64 0.117 - 0.175: 8 0.175 - 0.233: 6 0.233 - 0.292: 6 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ASN A 14 " pdb=" N ASN A 14 " pdb=" C ASN A 14 " pdb=" CB ASN A 14 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA ASN C 14 " pdb=" N ASN C 14 " pdb=" C ASN C 14 " pdb=" CB ASN C 14 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA ASN I 14 " pdb=" N ASN I 14 " pdb=" C ASN I 14 " pdb=" CB ASN I 14 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 489 not shown) Planarity restraints: 534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR J 36 " 0.018 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C THR J 36 " -0.055 2.00e-02 2.50e+03 pdb=" O THR J 36 " 0.018 2.00e-02 2.50e+03 pdb=" N TYC J 37 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 36 " 0.018 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C THR I 36 " -0.055 2.00e-02 2.50e+03 pdb=" O THR I 36 " 0.018 2.00e-02 2.50e+03 pdb=" N TYC I 37 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR L 36 " 0.018 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C THR L 36 " -0.055 2.00e-02 2.50e+03 pdb=" O THR L 36 " 0.017 2.00e-02 2.50e+03 pdb=" N TYC L 37 " 0.019 2.00e-02 2.50e+03 ... (remaining 531 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 8 2.30 - 2.95: 1547 2.95 - 3.60: 3923 3.60 - 4.25: 6523 4.25 - 4.90: 11207 Nonbonded interactions: 23208 Sorted by model distance: nonbonded pdb=" OG1 THR C 6 " pdb=" N THR B 6 " model vdw 1.654 2.520 nonbonded pdb=" N THR I 6 " pdb=" OG1 THR J 6 " model vdw 1.802 2.520 nonbonded pdb=" CG2 THR B 6 " pdb=" NH1 ARG D 11 " model vdw 1.997 3.540 nonbonded pdb=" CB THR C 4 " pdb=" O THR B 4 " model vdw 2.009 3.470 nonbonded pdb=" O THR I 4 " pdb=" CB THR J 4 " model vdw 2.203 3.470 ... (remaining 23203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'I' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'K' } 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: 0.800 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: 0.040 Set scattering table: 0.040 Process input model: 12.160 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 : 0.011 0.125 2994 Z= 0.602 Angle : 2.221 29.653 4068 Z= 1.224 Chirality : 0.061 0.292 492 Planarity : 0.005 0.032 534 Dihedral : 12.082 51.508 984 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -4.03 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 18 PHE 0.011 0.002 PHE E 15 ARG 0.001 0.000 ARG K 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.345 Fit side-chains REVERT: J 11 ARG cc_start: 0.7375 (mtt180) cc_final: 0.6689 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1284 time to fit residues: 7.5203 Evaluate side-chains 29 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 0.0170 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 overall best weight: 1.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN B 3 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2994 Z= 0.185 Angle : 0.480 6.893 4068 Z= 0.239 Chirality : 0.043 0.125 492 Planarity : 0.002 0.015 534 Dihedral : 7.964 44.802 432 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.85 % Allowed : 8.64 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 18 PHE 0.007 0.001 PHE K 15 ARG 0.001 0.000 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.349 Fit side-chains REVERT: F 11 ARG cc_start: 0.7689 (mtt180) cc_final: 0.6777 (pmt-80) REVERT: D 11 ARG cc_start: 0.7981 (mtt180) cc_final: 0.6403 (pmt-80) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 0.1404 time to fit residues: 8.6731 Evaluate side-chains 38 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain D residue 34 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.0020 chunk 18 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 GLN J 3 ASN ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2994 Z= 0.216 Angle : 0.510 8.969 4068 Z= 0.243 Chirality : 0.043 0.127 492 Planarity : 0.002 0.012 534 Dihedral : 5.949 28.650 432 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.47 % Allowed : 15.12 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 18 PHE 0.007 0.001 PHE K 15 ARG 0.001 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.332 Fit side-chains REVERT: A 11 ARG cc_start: 0.7466 (mtt180) cc_final: 0.6764 (pmt-80) REVERT: F 11 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7013 (pmt-80) REVERT: D 11 ARG cc_start: 0.8214 (mtt180) cc_final: 0.6730 (pmt-80) outliers start: 8 outliers final: 8 residues processed: 54 average time/residue: 0.1533 time to fit residues: 10.0800 Evaluate side-chains 51 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain D residue 34 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 GLN ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2994 Z= 0.180 Angle : 0.568 9.296 4068 Z= 0.245 Chirality : 0.043 0.126 492 Planarity : 0.002 0.010 534 Dihedral : 5.671 26.122 432 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.78 % Allowed : 19.75 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 18 PHE 0.006 0.001 PHE K 15 ARG 0.001 0.000 ARG L 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.341 Fit side-chains REVERT: A 11 ARG cc_start: 0.7503 (mtt180) cc_final: 0.6747 (pmt-80) REVERT: F 11 ARG cc_start: 0.7907 (mtt180) cc_final: 0.6910 (pmt-80) REVERT: D 11 ARG cc_start: 0.8202 (mtt180) cc_final: 0.6647 (pmt-80) outliers start: 9 outliers final: 9 residues processed: 54 average time/residue: 0.1582 time to fit residues: 10.3092 Evaluate side-chains 49 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain D residue 34 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 ASN C 10 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2994 Z= 0.297 Angle : 0.586 8.131 4068 Z= 0.273 Chirality : 0.043 0.132 492 Planarity : 0.002 0.014 534 Dihedral : 6.714 35.462 432 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.40 % Allowed : 20.37 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS J 18 PHE 0.010 0.002 PHE D 15 ARG 0.002 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.358 Fit side-chains REVERT: K 22 ASN cc_start: 0.8408 (t0) cc_final: 0.8168 (t0) REVERT: A 11 ARG cc_start: 0.7533 (mtt180) cc_final: 0.6809 (pmt-80) REVERT: J 11 ARG cc_start: 0.7371 (mtt180) cc_final: 0.7043 (pmt-80) REVERT: J 12 LEU cc_start: 0.8807 (mm) cc_final: 0.8603 (mm) REVERT: D 11 ARG cc_start: 0.8376 (mtt180) cc_final: 0.7222 (pmt-80) outliers start: 11 outliers final: 8 residues processed: 49 average time/residue: 0.1728 time to fit residues: 10.1469 Evaluate side-chains 48 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN J 3 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 2994 Z= 0.457 Angle : 0.726 9.658 4068 Z= 0.343 Chirality : 0.047 0.143 492 Planarity : 0.004 0.019 534 Dihedral : 7.698 40.678 432 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.94 % Favored : 88.06 % Rotamer: Outliers : 3.70 % Allowed : 20.37 % 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: -4.73 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.004 HIS A 18 PHE 0.016 0.003 PHE D 15 ARG 0.002 0.000 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7309 (mtt180) cc_final: 0.6925 (pmt-80) REVERT: F 11 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7239 (pmt-80) REVERT: J 11 ARG cc_start: 0.7363 (mtt180) cc_final: 0.7101 (pmt-80) REVERT: D 11 ARG cc_start: 0.8387 (mtt180) cc_final: 0.7390 (pmt-80) outliers start: 12 outliers final: 11 residues processed: 50 average time/residue: 0.1635 time to fit residues: 9.8877 Evaluate side-chains 49 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 0.0020 chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2994 Z= 0.116 Angle : 0.574 9.233 4068 Z= 0.243 Chirality : 0.044 0.127 492 Planarity : 0.001 0.007 534 Dihedral : 5.496 29.240 432 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.47 % Allowed : 21.30 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.006 0.001 PHE D 15 ARG 0.001 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 22 ASN cc_start: 0.8351 (t0) cc_final: 0.8144 (t0) REVERT: F 11 ARG cc_start: 0.7891 (mtt180) cc_final: 0.7037 (pmt-80) REVERT: J 11 ARG cc_start: 0.7362 (mtt180) cc_final: 0.7074 (pmt-80) REVERT: D 11 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7409 (pmt-80) outliers start: 8 outliers final: 7 residues processed: 55 average time/residue: 0.1479 time to fit residues: 9.7735 Evaluate side-chains 50 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain H residue 34 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.0010 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2994 Z= 0.222 Angle : 0.625 10.107 4068 Z= 0.265 Chirality : 0.043 0.131 492 Planarity : 0.002 0.009 534 Dihedral : 6.290 30.999 432 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.78 % Allowed : 22.84 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 18 PHE 0.010 0.001 PHE D 15 ARG 0.001 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 22 ASN cc_start: 0.8405 (t0) cc_final: 0.8167 (t0) REVERT: A 11 ARG cc_start: 0.7349 (mtt180) cc_final: 0.6898 (pmt-80) REVERT: F 11 ARG cc_start: 0.7987 (mtt180) cc_final: 0.7097 (pmt-80) REVERT: J 11 ARG cc_start: 0.7358 (mtt180) cc_final: 0.7088 (pmt-80) REVERT: D 11 ARG cc_start: 0.8273 (mtt180) cc_final: 0.7411 (pmt-80) outliers start: 9 outliers final: 8 residues processed: 51 average time/residue: 0.1570 time to fit residues: 9.6579 Evaluate side-chains 50 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain G residue 29 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 25 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2994 Z= 0.128 Angle : 0.597 9.873 4068 Z= 0.243 Chirality : 0.043 0.124 492 Planarity : 0.001 0.005 534 Dihedral : 5.336 28.767 432 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.78 % Allowed : 23.46 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 18 PHE 0.007 0.001 PHE D 15 ARG 0.001 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 11 ARG cc_start: 0.7902 (mtt180) cc_final: 0.6983 (pmt-80) REVERT: J 11 ARG cc_start: 0.7297 (mtt180) cc_final: 0.7056 (pmt-80) REVERT: D 11 ARG cc_start: 0.8198 (mtt180) cc_final: 0.7253 (pmt-80) outliers start: 9 outliers final: 9 residues processed: 50 average time/residue: 0.1401 time to fit residues: 8.5846 Evaluate side-chains 48 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 21 ASN Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2994 Z= 0.363 Angle : 0.696 10.080 4068 Z= 0.310 Chirality : 0.045 0.140 492 Planarity : 0.003 0.014 534 Dihedral : 7.088 37.683 432 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.72 % Favored : 85.28 % Rotamer: Outliers : 3.09 % Allowed : 22.84 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS A 18 PHE 0.015 0.002 PHE D 15 ARG 0.002 0.000 ARG A 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7357 (mtt180) cc_final: 0.6975 (pmt-80) REVERT: A 34 SER cc_start: 0.7599 (p) cc_final: 0.7388 (m) REVERT: J 11 ARG cc_start: 0.7352 (mtt180) cc_final: 0.7083 (pmt-80) REVERT: D 11 ARG cc_start: 0.8426 (mtt180) cc_final: 0.7320 (pmt-80) outliers start: 10 outliers final: 10 residues processed: 49 average time/residue: 0.1419 time to fit residues: 8.5344 Evaluate side-chains 50 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 21 ASN Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.097709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.080110 restraints weight = 6564.378| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.04 r_work: 0.3653 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2994 Z= 0.280 Angle : 0.660 10.015 4068 Z= 0.287 Chirality : 0.044 0.140 492 Planarity : 0.002 0.011 534 Dihedral : 6.590 32.585 432 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 4.32 % Allowed : 22.22 % 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: -4.81 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 18 PHE 0.013 0.002 PHE D 15 ARG 0.001 0.000 ARG J 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1178.70 seconds wall clock time: 21 minutes 58.48 seconds (1318.48 seconds total)