Starting phenix.real_space_refine on Sun Mar 10 14:36:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az0_15728/03_2024/8az0_15728_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az0_15728/03_2024/8az0_15728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az0_15728/03_2024/8az0_15728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az0_15728/03_2024/8az0_15728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az0_15728/03_2024/8az0_15728_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az0_15728/03_2024/8az0_15728_updated.pdb" } resolution = 3.4 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: 3 Type Number sf(0) Gaussians C 1350 2.51 5 N 420 2.21 5 O 410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 37": "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: 2180 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "B" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "C" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "D" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "E" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "F" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "G" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "H" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "I" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "J" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Time building chain proxies: 2.50, per 1000 atoms: 1.15 Number of scatterers: 2180 At special positions: 0 Unit cell: (63, 73.08, 45.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 410 8.00 N 420 7.00 C 1350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 715.5 milliseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 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: 0.31 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: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 340 1.29 - 1.35: 410 1.35 - 1.41: 270 1.41 - 1.48: 306 1.48 - 1.54: 904 Bond restraints: 2230 Sorted by residual: bond pdb=" N THR G 36 " pdb=" CA THR G 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.76e+00 bond pdb=" N THR J 36 " pdb=" CA THR J 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.73e+00 bond pdb=" N THR B 36 " pdb=" CA THR B 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.68e+00 bond pdb=" N THR H 36 " pdb=" CA THR H 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.62e+00 bond pdb=" N THR E 36 " pdb=" CA THR E 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.62e+00 ... (remaining 2225 not shown) Histogram of bond angle deviations from ideal: 106.04 - 111.07: 917 111.07 - 116.10: 470 116.10 - 121.14: 970 121.14 - 126.17: 663 126.17 - 131.20: 20 Bond angle restraints: 3040 Sorted by residual: angle pdb=" CA SER B 34 " pdb=" C SER B 34 " pdb=" O SER B 34 " ideal model delta sigma weight residual 121.28 117.78 3.50 1.19e+00 7.06e-01 8.64e+00 angle pdb=" CA SER A 34 " pdb=" C SER A 34 " pdb=" O SER A 34 " ideal model delta sigma weight residual 121.28 117.80 3.48 1.19e+00 7.06e-01 8.57e+00 angle pdb=" CA SER J 34 " pdb=" C SER J 34 " pdb=" O SER J 34 " ideal model delta sigma weight residual 121.28 117.81 3.47 1.19e+00 7.06e-01 8.49e+00 angle pdb=" CA SER G 34 " pdb=" C SER G 34 " pdb=" O SER G 34 " ideal model delta sigma weight residual 121.28 117.81 3.47 1.19e+00 7.06e-01 8.49e+00 angle pdb=" CA SER D 34 " pdb=" C SER D 34 " pdb=" O SER D 34 " ideal model delta sigma weight residual 121.28 117.83 3.45 1.19e+00 7.06e-01 8.42e+00 ... (remaining 3035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.96: 1022 5.96 - 11.92: 128 11.92 - 17.87: 72 17.87 - 23.83: 28 23.83 - 29.79: 10 Dihedral angle restraints: 1260 sinusoidal: 440 harmonic: 820 Sorted by residual: dihedral pdb=" N HIS J 18 " pdb=" CA AHIS J 18 " pdb=" CB AHIS J 18 " pdb=" CG AHIS J 18 " ideal model delta sinusoidal sigma weight residual -60.00 -83.02 23.02 3 1.50e+01 4.44e-03 3.05e+00 dihedral pdb=" N HIS E 18 " pdb=" CA AHIS E 18 " pdb=" CB AHIS E 18 " pdb=" CG AHIS E 18 " ideal model delta sinusoidal sigma weight residual -60.00 -83.00 23.00 3 1.50e+01 4.44e-03 3.04e+00 dihedral pdb=" N HIS D 18 " pdb=" CA AHIS D 18 " pdb=" CB AHIS D 18 " pdb=" CG AHIS D 18 " ideal model delta sinusoidal sigma weight residual -60.00 -82.99 22.99 3 1.50e+01 4.44e-03 3.04e+00 ... (remaining 1257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 127 0.027 - 0.054: 149 0.054 - 0.080: 24 0.080 - 0.107: 17 0.107 - 0.134: 23 Chirality restraints: 340 Sorted by residual: chirality pdb=" CA ILE F 26 " pdb=" N ILE F 26 " pdb=" C ILE F 26 " pdb=" CB ILE F 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 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 4.24e-01 ... (remaining 337 not shown) Planarity restraints: 410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 32 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.77e+00 pdb=" C VAL D 32 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL D 32 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY D 33 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 32 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C VAL B 32 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL B 32 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY B 33 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 32 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.67e+00 pdb=" C VAL I 32 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL I 32 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY I 33 " 0.017 2.00e-02 2.50e+03 ... (remaining 407 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 1535 3.07 - 3.53: 2009 3.53 - 3.98: 3241 3.98 - 4.44: 3958 4.44 - 4.90: 7332 Nonbonded interactions: 18075 Sorted by model distance: nonbonded pdb=" O SER B 34 " pdb=" OG SER B 34 " model vdw 2.611 2.440 nonbonded pdb=" O SER J 34 " pdb=" OG SER J 34 " model vdw 2.612 2.440 nonbonded pdb=" O SER F 34 " pdb=" OG SER F 34 " model vdw 2.612 2.440 nonbonded pdb=" O SER H 34 " pdb=" OG SER H 34 " model vdw 2.612 2.440 nonbonded pdb=" O SER D 34 " pdb=" OG SER D 34 " model vdw 2.612 2.440 ... (remaining 18070 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' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'B' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'C' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'D' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'E' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'F' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'G' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'H' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'I' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'J' and (resid 10 through 17 or resid 19 through 38)) } 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=0.50 max=1.00 mean=0.97 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: 1.100 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: 0.000 Extract box with map and model: 5.360 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.040 Find NCS groups from input model: 0.180 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.006 0.032 2230 Z= 0.360 Angle : 0.743 4.601 3040 Z= 0.491 Chirality : 0.051 0.134 340 Planarity : 0.005 0.030 410 Dihedral : 8.049 29.789 740 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % 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: -4.46 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 23 TYR 0.003 0.001 TYR E 37 ARG 0.000 0.000 ARG E 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.230 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0725 time to fit residues: 1.5391 Evaluate side-chains 13 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.0470 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A A 21 ASN B 18 HIS A B 21 ASN C 18 HIS A C 21 ASN D 18 HIS A D 21 ASN E 21 ASN F 18 HIS A F 21 ASN G 21 ASN H 18 HIS A H 21 ASN I 21 ASN J 21 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 2230 Z= 0.161 Angle : 0.391 2.400 3040 Z= 0.224 Chirality : 0.043 0.124 340 Planarity : 0.002 0.004 410 Dihedral : 3.541 7.667 310 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 0.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -4.53 (0.22), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.17), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE H 15 TYR 0.002 0.001 TYR B 37 ARG 0.000 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.240 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0701 time to fit residues: 1.7079 Evaluate side-chains 15 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.021 2230 Z= 0.305 Angle : 0.533 3.383 3040 Z= 0.293 Chirality : 0.045 0.122 340 Planarity : 0.003 0.008 410 Dihedral : 4.184 9.283 310 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.42 % Allowed : 5.00 % Favored : 94.58 % 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: -4.57 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.003 PHE H 15 TYR 0.003 0.001 TYR I 37 ARG 0.001 0.000 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.245 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.0713 time to fit residues: 3.4096 Evaluate side-chains 28 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2230 Z= 0.137 Angle : 0.425 3.233 3040 Z= 0.228 Chirality : 0.043 0.124 340 Planarity : 0.001 0.004 410 Dihedral : 3.498 8.215 310 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.67 % Allowed : 8.33 % Favored : 90.00 % 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: -4.64 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE H 15 TYR 0.002 0.001 TYR G 37 ARG 0.000 0.000 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.314 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 26 average time/residue: 0.0965 time to fit residues: 3.7250 Evaluate side-chains 29 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 16 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 0.0370 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2230 Z= 0.110 Angle : 0.394 3.044 3040 Z= 0.211 Chirality : 0.043 0.120 340 Planarity : 0.001 0.003 410 Dihedral : 3.245 7.693 310 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.67 % Allowed : 9.58 % Favored : 88.75 % 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: -4.57 (0.31), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.24), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE H 15 TYR 0.003 0.000 TYR G 37 ARG 0.000 0.000 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.250 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 28 average time/residue: 0.0737 time to fit residues: 2.9716 Evaluate side-chains 32 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.014 2230 Z= 0.175 Angle : 0.436 3.302 3040 Z= 0.235 Chirality : 0.043 0.122 340 Planarity : 0.002 0.004 410 Dihedral : 3.534 8.347 310 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 3.33 % Allowed : 8.33 % Favored : 88.33 % 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: -4.65 (0.32), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.24), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE H 15 TYR 0.003 0.001 TYR G 37 ARG 0.000 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 29 time to evaluate : 0.243 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 30 average time/residue: 0.0707 time to fit residues: 3.0416 Evaluate side-chains 36 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain J residue 28 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.017 2230 Z= 0.225 Angle : 0.481 3.679 3040 Z= 0.258 Chirality : 0.044 0.123 340 Planarity : 0.002 0.007 410 Dihedral : 3.804 8.771 310 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 3.33 % Allowed : 10.42 % Favored : 86.25 % 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: -4.53 (0.34), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.26), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE H 15 TYR 0.010 0.001 TYR G 37 ARG 0.001 0.000 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.229 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 29 average time/residue: 0.0653 time to fit residues: 2.7638 Evaluate side-chains 35 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 0.0050 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 2230 Z= 0.098 Angle : 0.407 3.541 3040 Z= 0.213 Chirality : 0.043 0.119 340 Planarity : 0.001 0.007 410 Dihedral : 3.253 7.076 310 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.50 % Allowed : 11.25 % Favored : 86.25 % 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: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.26), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE G 23 TYR 0.009 0.001 TYR F 37 ARG 0.000 0.000 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.220 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 29 average time/residue: 0.0724 time to fit residues: 3.0021 Evaluate side-chains 35 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 28 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.5013 > 50: distance: 90 - 99: 15.131 distance: 99 - 100: 12.703 distance: 100 - 101: 14.555 distance: 100 - 103: 13.229 distance: 101 - 102: 14.653 distance: 101 - 105: 12.908 distance: 103 - 104: 18.378 distance: 105 - 106: 11.115 distance: 106 - 107: 5.554 distance: 107 - 108: 3.423 distance: 107 - 109: 6.250 distance: 109 - 110: 6.848 distance: 110 - 111: 10.702 distance: 110 - 113: 5.887 distance: 111 - 112: 8.221 distance: 113 - 114: 11.590 distance: 114 - 115: 7.804 distance: 114 - 116: 25.806 distance: 117 - 118: 8.080 distance: 118 - 119: 4.230 distance: 119 - 120: 7.143 distance: 119 - 125: 10.160 distance: 121 - 122: 6.990 distance: 122 - 123: 7.495 distance: 122 - 124: 15.644 distance: 125 - 126: 3.067 distance: 126 - 129: 6.522 distance: 127 - 128: 3.276 distance: 127 - 136: 7.760 distance: 129 - 130: 4.364 distance: 130 - 132: 12.380 distance: 131 - 133: 7.233 distance: 132 - 134: 10.103 distance: 133 - 135: 15.281 distance: 136 - 137: 16.212 distance: 137 - 138: 7.113 distance: 138 - 139: 9.740 distance: 138 - 140: 5.801 distance: 140 - 141: 4.568 distance: 141 - 142: 14.032 distance: 141 - 144: 16.636 distance: 145 - 146: 17.828 distance: 146 - 147: 15.210 distance: 146 - 149: 12.522 distance: 147 - 148: 35.536 distance: 147 - 153: 31.689 distance: 149 - 150: 8.936 distance: 149 - 151: 33.795 distance: 150 - 152: 23.580 distance: 154 - 155: 29.430 distance: 154 - 157: 18.530 distance: 155 - 156: 20.846 distance: 157 - 158: 45.284 distance: 158 - 159: 23.588 distance: 158 - 160: 26.301 distance: 161 - 162: 12.660 distance: 162 - 163: 8.381 distance: 162 - 165: 20.381 distance: 163 - 164: 23.469 distance: 163 - 167: 5.659 distance: 165 - 166: 14.070