Starting phenix.real_space_refine on Sun Mar 10 14:49:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/03_2024/7m62_23687_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/03_2024/7m62_23687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/03_2024/7m62_23687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/03_2024/7m62_23687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/03_2024/7m62_23687_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/03_2024/7m62_23687_updated.pdb" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 1.000 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 10 5.16 5 C 1450 2.51 5 N 440 2.21 5 O 480 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: 2380 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 31} Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 31} Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 31} Chain: "D" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 31} Chain: "E" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 31} Chain: "F" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 31} Chain: "G" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 31} Chain: "H" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 31} Chain: "I" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 31} Chain: "J" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 31} Time building chain proxies: 1.71, per 1000 atoms: 0.72 Number of scatterers: 2380 At special positions: 0 Unit cell: (68.575, 72.795, 41.145, 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 10 16.00 O 480 8.00 N 440 7.00 C 1450 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: 1.00 Conformation dependent library (CDL) restraints added in 431.3 milliseconds 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 600 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: 0.32 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: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 380 1.31 - 1.44: 740 1.44 - 1.56: 1280 1.56 - 1.68: 0 1.68 - 1.81: 10 Bond restraints: 2410 Sorted by residual: bond pdb=" CB ASN G 22 " pdb=" CG ASN G 22 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" CB ASN H 22 " pdb=" CG ASN H 22 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" CB ASN J 22 " pdb=" CG ASN J 22 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" CB ASN I 22 " pdb=" CG ASN I 22 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" CB ASN A 22 " pdb=" CG ASN A 22 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.01e+01 ... (remaining 2405 not shown) Histogram of bond angle deviations from ideal: 105.63 - 110.74: 754 110.74 - 115.85: 813 115.85 - 120.95: 902 120.95 - 126.06: 791 126.06 - 131.17: 20 Bond angle restraints: 3280 Sorted by residual: angle pdb=" N ASN F 22 " pdb=" CA ASN F 22 " pdb=" C ASN F 22 " ideal model delta sigma weight residual 109.80 114.78 -4.98 1.70e+00 3.46e-01 8.59e+00 angle pdb=" N ASN B 22 " pdb=" CA ASN B 22 " pdb=" C ASN B 22 " ideal model delta sigma weight residual 109.80 114.78 -4.98 1.70e+00 3.46e-01 8.58e+00 angle pdb=" N ASN J 22 " pdb=" CA ASN J 22 " pdb=" C ASN J 22 " ideal model delta sigma weight residual 109.80 114.77 -4.97 1.70e+00 3.46e-01 8.54e+00 angle pdb=" N ASN E 22 " pdb=" CA ASN E 22 " pdb=" C ASN E 22 " ideal model delta sigma weight residual 109.80 114.75 -4.95 1.70e+00 3.46e-01 8.49e+00 angle pdb=" N ASN D 22 " pdb=" CA ASN D 22 " pdb=" C ASN D 22 " ideal model delta sigma weight residual 109.80 114.75 -4.95 1.70e+00 3.46e-01 8.49e+00 ... (remaining 3275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.29: 1110 11.29 - 22.58: 160 22.58 - 33.87: 70 33.87 - 45.17: 30 45.17 - 56.46: 10 Dihedral angle restraints: 1380 sinusoidal: 460 harmonic: 920 Sorted by residual: dihedral pdb=" CA ASN I 21 " pdb=" C ASN I 21 " pdb=" N ASN I 22 " pdb=" CA ASN I 22 " ideal model delta harmonic sigma weight residual -180.00 -152.47 -27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ASN G 21 " pdb=" C ASN G 21 " pdb=" N ASN G 22 " pdb=" CA ASN G 22 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ASN A 21 " pdb=" C ASN A 21 " pdb=" N ASN A 22 " pdb=" CA ASN A 22 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 1377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 299 0.059 - 0.118: 71 0.118 - 0.177: 10 0.177 - 0.236: 10 0.236 - 0.295: 10 Chirality restraints: 400 Sorted by residual: chirality pdb=" CB ILE H 26 " pdb=" CA ILE H 26 " pdb=" CG1 ILE H 26 " pdb=" CG2 ILE H 26 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE C 26 " pdb=" CA ILE C 26 " pdb=" CG1 ILE C 26 " pdb=" CG2 ILE C 26 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB ILE D 26 " pdb=" CA ILE D 26 " pdb=" CG1 ILE D 26 " pdb=" CG2 ILE D 26 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 397 not shown) Planarity restraints: 430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 20 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.31e+00 pdb=" C SER D 20 " 0.020 2.00e-02 2.50e+03 pdb=" O SER D 20 " -0.008 2.00e-02 2.50e+03 pdb=" N ASN D 21 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 20 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C SER H 20 " 0.020 2.00e-02 2.50e+03 pdb=" O SER H 20 " -0.007 2.00e-02 2.50e+03 pdb=" N ASN H 21 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 20 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C SER C 20 " -0.020 2.00e-02 2.50e+03 pdb=" O SER C 20 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN C 21 " 0.007 2.00e-02 2.50e+03 ... (remaining 427 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 788 2.84 - 3.35: 2458 3.35 - 3.87: 4304 3.87 - 4.38: 4606 4.38 - 4.90: 9088 Nonbonded interactions: 21244 Sorted by model distance: nonbonded pdb=" O ASN A 22 " pdb=" N NH2 D 38 " model vdw 2.321 3.120 nonbonded pdb=" N NH2 B 38 " pdb=" O ASN E 22 " model vdw 2.321 3.120 nonbonded pdb=" O ASN C 22 " pdb=" N NH2 H 38 " model vdw 2.321 3.120 nonbonded pdb=" N NH2 F 38 " pdb=" O ASN I 22 " model vdw 2.321 3.120 nonbonded pdb=" O ASN B 22 " pdb=" N NH2 C 38 " model vdw 2.325 3.120 ... (remaining 21239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 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: 0.570 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.480 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 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 : 0.007 0.079 2410 Z= 0.323 Angle : 1.131 5.506 3280 Z= 0.652 Chirality : 0.073 0.295 400 Planarity : 0.003 0.011 430 Dihedral : 14.835 56.457 780 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 32.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.33 % Favored : 76.67 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.31), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.24), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS J 18 PHE 0.008 0.003 PHE D 23 TYR 0.003 0.001 TYR H 37 ARG 0.001 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.307 Fit side-chains REVERT: A 14 ASN cc_start: 0.8754 (t0) cc_final: 0.8460 (t0) REVERT: B 14 ASN cc_start: 0.8716 (t0) cc_final: 0.8419 (t0) REVERT: C 14 ASN cc_start: 0.8789 (t0) cc_final: 0.8472 (t0) REVERT: D 14 ASN cc_start: 0.8791 (t0) cc_final: 0.8472 (t0) REVERT: E 14 ASN cc_start: 0.8779 (t0) cc_final: 0.8464 (t0) REVERT: F 14 ASN cc_start: 0.8778 (t0) cc_final: 0.8458 (t0) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2937 time to fit residues: 12.9960 Evaluate side-chains 20 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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: 9.9990 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 50.0000 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 50.0000 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 21 ASN B 14 ASN B 21 ASN C 14 ASN C 21 ASN D 14 ASN D 21 ASN E 14 ASN E 21 ASN F 14 ASN F 21 ASN G 21 ASN 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: 0.6404 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2410 Z= 0.182 Angle : 0.946 7.990 3280 Z= 0.526 Chirality : 0.054 0.167 400 Planarity : 0.004 0.021 430 Dihedral : 12.086 34.597 330 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.33 % Favored : 80.67 % Rotamer: Outliers : 5.93 % Allowed : 17.04 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.94 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.018 0.003 PHE A 23 TYR 0.009 0.002 TYR G 37 ARG 0.004 0.001 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 22 time to evaluate : 0.298 Fit side-chains REVERT: C 14 ASN cc_start: 0.8897 (t0) cc_final: 0.8596 (t0) REVERT: D 14 ASN cc_start: 0.8901 (t0) cc_final: 0.8598 (t0) REVERT: E 14 ASN cc_start: 0.8586 (t0) cc_final: 0.7958 (t0) REVERT: F 14 ASN cc_start: 0.8585 (t0) cc_final: 0.7958 (t0) outliers start: 16 outliers final: 10 residues processed: 34 average time/residue: 0.1244 time to fit residues: 5.3355 Evaluate side-chains 28 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 18 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 22 ASN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 22 ASN Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 22 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 0.0970 chunk 29 optimal weight: 30.0000 chunk 24 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 21 optimal weight: 40.0000 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 overall best weight: 4.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN D 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2410 Z= 0.130 Angle : 0.882 7.097 3280 Z= 0.486 Chirality : 0.053 0.270 400 Planarity : 0.003 0.013 430 Dihedral : 11.634 32.844 330 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.33 % Favored : 80.67 % Rotamer: Outliers : 5.19 % Allowed : 18.52 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.37), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 18 PHE 0.010 0.002 PHE A 23 TYR 0.005 0.001 TYR H 37 ARG 0.003 0.001 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 16 time to evaluate : 0.286 Fit side-chains REVERT: A 14 ASN cc_start: 0.8827 (t0) cc_final: 0.8363 (t0) REVERT: B 14 ASN cc_start: 0.8805 (t0) cc_final: 0.8337 (t0) REVERT: C 14 ASN cc_start: 0.8934 (t0) cc_final: 0.8495 (t0) REVERT: D 14 ASN cc_start: 0.8942 (t0) cc_final: 0.8506 (t0) REVERT: E 14 ASN cc_start: 0.8749 (t0) cc_final: 0.8312 (t0) REVERT: F 14 ASN cc_start: 0.8751 (t0) cc_final: 0.8301 (t0) REVERT: G 11 ARG cc_start: 0.2751 (pmt-80) cc_final: 0.1751 (pmt-80) REVERT: I 14 ASN cc_start: 0.8929 (t0) cc_final: 0.8583 (t0) REVERT: J 14 ASN cc_start: 0.8926 (t0) cc_final: 0.8565 (t0) outliers start: 14 outliers final: 8 residues processed: 30 average time/residue: 0.1288 time to fit residues: 4.8788 Evaluate side-chains 22 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 14 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 22 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 18 optimal weight: 30.0000 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: 0.6389 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2410 Z= 0.160 Angle : 0.914 7.519 3280 Z= 0.500 Chirality : 0.055 0.314 400 Planarity : 0.003 0.011 430 Dihedral : 11.559 32.114 330 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.00 % Favored : 78.00 % Rotamer: Outliers : 11.85 % Allowed : 17.78 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -4.54 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 18 PHE 0.009 0.002 PHE B 23 TYR 0.007 0.001 TYR H 37 ARG 0.002 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 20 time to evaluate : 0.306 Fit side-chains REVERT: A 14 ASN cc_start: 0.8846 (t0) cc_final: 0.8410 (t0) REVERT: B 14 ASN cc_start: 0.8844 (t0) cc_final: 0.8405 (t0) REVERT: C 14 ASN cc_start: 0.8920 (t0) cc_final: 0.8529 (t0) REVERT: D 14 ASN cc_start: 0.8922 (t0) cc_final: 0.8529 (t0) REVERT: E 14 ASN cc_start: 0.8647 (t0) cc_final: 0.8232 (t0) REVERT: F 14 ASN cc_start: 0.8647 (t0) cc_final: 0.8238 (t0) REVERT: G 11 ARG cc_start: 0.2999 (pmt-80) cc_final: 0.2074 (pmt-80) REVERT: H 11 ARG cc_start: 0.3074 (pmt-80) cc_final: 0.2120 (pmt-80) REVERT: I 14 ASN cc_start: 0.9008 (t0) cc_final: 0.8754 (t0) REVERT: J 14 ASN cc_start: 0.9008 (t0) cc_final: 0.8752 (t0) outliers start: 32 outliers final: 26 residues processed: 50 average time/residue: 0.0978 time to fit residues: 6.2415 Evaluate side-chains 42 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 16 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain J residue 22 ASN Chi-restraints excluded: chain J residue 30 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 40.0000 chunk 11 optimal weight: 30.0000 chunk 24 optimal weight: 40.0000 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 70.0000 chunk 14 optimal weight: 30.0000 chunk 26 optimal weight: 0.0040 chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 17 optimal weight: 7.9990 overall best weight: 6.8000 ------------------------------------------------------------------------------- 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: 0.6368 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2410 Z= 0.154 Angle : 0.907 7.222 3280 Z= 0.493 Chirality : 0.058 0.374 400 Planarity : 0.003 0.010 430 Dihedral : 11.458 29.923 330 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 25.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.67 % Favored : 81.33 % Rotamer: Outliers : 9.63 % Allowed : 21.48 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.37), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.29), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.009 0.002 PHE A 15 TYR 0.005 0.001 TYR G 37 ARG 0.001 0.000 ARG E 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 22 time to evaluate : 0.285 Fit side-chains REVERT: A 14 ASN cc_start: 0.8933 (t0) cc_final: 0.8516 (t0) REVERT: B 14 ASN cc_start: 0.8932 (t0) cc_final: 0.8507 (t0) REVERT: C 14 ASN cc_start: 0.8817 (t0) cc_final: 0.8210 (t0) REVERT: C 26 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6836 (pt) REVERT: D 14 ASN cc_start: 0.8820 (t0) cc_final: 0.8298 (t0) REVERT: D 26 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6835 (pt) REVERT: E 14 ASN cc_start: 0.8688 (t0) cc_final: 0.8304 (t0) REVERT: F 14 ASN cc_start: 0.8688 (t0) cc_final: 0.8307 (t0) REVERT: G 11 ARG cc_start: 0.3278 (pmt-80) cc_final: 0.2564 (pmt-80) REVERT: G 14 ASN cc_start: 0.7617 (t0) cc_final: 0.7401 (t0) REVERT: H 11 ARG cc_start: 0.3277 (pmt-80) cc_final: 0.2561 (pmt-80) REVERT: H 14 ASN cc_start: 0.7616 (t0) cc_final: 0.7380 (t0) REVERT: I 14 ASN cc_start: 0.9007 (t0) cc_final: 0.8694 (t0) REVERT: J 14 ASN cc_start: 0.9007 (t0) cc_final: 0.8694 (t0) outliers start: 26 outliers final: 18 residues processed: 44 average time/residue: 0.1100 time to fit residues: 6.1432 Evaluate side-chains 40 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 20 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 22 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 30.0000 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 9 optimal weight: 50.0000 chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 0.0170 chunk 3 optimal weight: 40.0000 chunk 16 optimal weight: 20.0000 chunk 21 optimal weight: 0.0370 overall best weight: 5.4104 ------------------------------------------------------------------------------- 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: 0.6333 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2410 Z= 0.131 Angle : 0.893 7.313 3280 Z= 0.483 Chirality : 0.055 0.353 400 Planarity : 0.002 0.010 430 Dihedral : 11.246 29.208 330 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 24.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 12.59 % Allowed : 20.00 % Favored : 67.41 % 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: -4.52 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 18 PHE 0.010 0.002 PHE I 23 TYR 0.005 0.001 TYR H 37 ARG 0.001 0.000 ARG E 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 22 time to evaluate : 0.296 Fit side-chains REVERT: A 14 ASN cc_start: 0.8944 (t0) cc_final: 0.8542 (t0) REVERT: B 14 ASN cc_start: 0.8941 (t0) cc_final: 0.8534 (t0) REVERT: C 14 ASN cc_start: 0.8849 (t0) cc_final: 0.8272 (t0) REVERT: D 14 ASN cc_start: 0.8851 (t0) cc_final: 0.8276 (t0) REVERT: E 14 ASN cc_start: 0.8689 (t0) cc_final: 0.8318 (t0) REVERT: F 14 ASN cc_start: 0.8688 (t0) cc_final: 0.8309 (t0) REVERT: G 11 ARG cc_start: 0.3428 (pmt-80) cc_final: 0.2542 (pmt-80) REVERT: G 14 ASN cc_start: 0.8038 (t0) cc_final: 0.7735 (t0) REVERT: H 11 ARG cc_start: 0.3450 (pmt-80) cc_final: 0.2607 (pmt-80) REVERT: H 14 ASN cc_start: 0.8034 (t0) cc_final: 0.7732 (t0) REVERT: J 14 ASN cc_start: 0.8986 (t0) cc_final: 0.8620 (t0) outliers start: 34 outliers final: 20 residues processed: 54 average time/residue: 0.1011 time to fit residues: 6.9393 Evaluate side-chains 38 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 18 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 19 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 50.0000 chunk 24 optimal weight: 40.0000 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 40.0000 chunk 17 optimal weight: 0.0060 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN I 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2410 Z= 0.116 Angle : 0.855 6.767 3280 Z= 0.466 Chirality : 0.051 0.204 400 Planarity : 0.002 0.010 430 Dihedral : 10.918 28.296 330 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 8.15 % Allowed : 22.96 % Favored : 68.89 % 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: -4.47 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 18 PHE 0.010 0.002 PHE E 23 TYR 0.004 0.001 TYR H 37 ARG 0.002 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 14 time to evaluate : 0.269 Fit side-chains REVERT: A 14 ASN cc_start: 0.8872 (t0) cc_final: 0.8456 (t0) REVERT: B 14 ASN cc_start: 0.8912 (t0) cc_final: 0.8459 (t0) REVERT: C 14 ASN cc_start: 0.8665 (t0) cc_final: 0.8154 (t0) REVERT: D 14 ASN cc_start: 0.8731 (t0) cc_final: 0.8186 (t0) REVERT: E 14 ASN cc_start: 0.8661 (t0) cc_final: 0.8304 (t0) REVERT: F 14 ASN cc_start: 0.8573 (t0) cc_final: 0.8164 (t0) REVERT: G 11 ARG cc_start: 0.3576 (pmt-80) cc_final: 0.2533 (pmt-80) REVERT: G 14 ASN cc_start: 0.8155 (t0) cc_final: 0.7888 (t0) REVERT: H 11 ARG cc_start: 0.3572 (pmt-80) cc_final: 0.2534 (pmt-80) REVERT: H 14 ASN cc_start: 0.8145 (t0) cc_final: 0.7887 (t0) REVERT: I 14 ASN cc_start: 0.8843 (t0) cc_final: 0.8566 (t0) REVERT: J 14 ASN cc_start: 0.8999 (t0) cc_final: 0.8628 (t0) outliers start: 22 outliers final: 17 residues processed: 36 average time/residue: 0.1381 time to fit residues: 6.2060 Evaluate side-chains 31 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 14 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain I residue 21 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 21 optimal weight: 30.0000 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 40.0000 chunk 17 optimal weight: 0.2980 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.6304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2410 Z= 0.130 Angle : 0.870 7.379 3280 Z= 0.471 Chirality : 0.050 0.211 400 Planarity : 0.002 0.009 430 Dihedral : 10.825 28.715 330 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.33 % Favored : 78.67 % Rotamer: Outliers : 10.00 % Allowed : 20.37 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 18 PHE 0.009 0.002 PHE F 23 TYR 0.005 0.001 TYR H 37 ARG 0.001 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 14 time to evaluate : 0.294 Fit side-chains REVERT: A 14 ASN cc_start: 0.8867 (t0) cc_final: 0.8418 (t0) REVERT: B 14 ASN cc_start: 0.8894 (t0) cc_final: 0.8426 (t0) REVERT: C 14 ASN cc_start: 0.8557 (t0) cc_final: 0.8091 (t0) REVERT: D 14 ASN cc_start: 0.8673 (t0) cc_final: 0.8206 (t0) REVERT: E 14 ASN cc_start: 0.8533 (t0) cc_final: 0.8220 (t0) REVERT: F 14 ASN cc_start: 0.8760 (t0) cc_final: 0.8180 (t0) REVERT: G 11 ARG cc_start: 0.3958 (pmt-80) cc_final: 0.2913 (pmt-80) REVERT: G 14 ASN cc_start: 0.8260 (t0) cc_final: 0.7996 (t0) REVERT: H 11 ARG cc_start: 0.3843 (pmt-80) cc_final: 0.2842 (pmt-80) REVERT: H 14 ASN cc_start: 0.8320 (t0) cc_final: 0.8079 (t0) REVERT: I 32 VAL cc_start: 0.3730 (OUTLIER) cc_final: 0.3438 (m) REVERT: J 14 ASN cc_start: 0.8943 (t0) cc_final: 0.8567 (t0) REVERT: J 32 VAL cc_start: 0.3733 (OUTLIER) cc_final: 0.3441 (m) outliers start: 27 outliers final: 20 residues processed: 41 average time/residue: 0.1109 time to fit residues: 5.7797 Evaluate side-chains 36 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 14 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 32 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 23 optimal weight: 0.0980 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 overall best weight: 4.8188 ------------------------------------------------------------------------------- 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: 0.6170 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2410 Z= 0.117 Angle : 0.842 6.919 3280 Z= 0.458 Chirality : 0.049 0.189 400 Planarity : 0.002 0.010 430 Dihedral : 10.659 28.412 330 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.67 % Favored : 81.33 % Rotamer: Outliers : 8.15 % Allowed : 21.48 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS H 18 PHE 0.010 0.002 PHE J 23 TYR 0.004 0.001 TYR H 37 ARG 0.001 0.000 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 12 time to evaluate : 0.325 Fit side-chains REVERT: A 14 ASN cc_start: 0.8876 (t0) cc_final: 0.8425 (t0) REVERT: B 14 ASN cc_start: 0.8886 (t0) cc_final: 0.8440 (t0) REVERT: C 14 ASN cc_start: 0.8654 (t0) cc_final: 0.8218 (t0) REVERT: D 14 ASN cc_start: 0.8712 (t0) cc_final: 0.8296 (t0) REVERT: E 14 ASN cc_start: 0.8569 (t0) cc_final: 0.8126 (t0) REVERT: F 14 ASN cc_start: 0.8537 (t0) cc_final: 0.8211 (t0) outliers start: 22 outliers final: 22 residues processed: 34 average time/residue: 0.0663 time to fit residues: 3.4411 Evaluate side-chains 33 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 11 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 22 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 30.0000 chunk 3 optimal weight: 40.0000 chunk 6 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 30.0000 chunk 24 optimal weight: 40.0000 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 17 optimal weight: 7.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.6764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2410 Z= 0.155 Angle : 0.891 7.287 3280 Z= 0.483 Chirality : 0.051 0.220 400 Planarity : 0.003 0.009 430 Dihedral : 10.791 29.033 330 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.33 % Favored : 78.67 % Rotamer: Outliers : 8.52 % Allowed : 21.11 % Favored : 70.37 % 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: -4.58 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 18 PHE 0.009 0.002 PHE G 15 TYR 0.006 0.001 TYR H 37 ARG 0.001 0.000 ARG G 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 14 time to evaluate : 0.309 Fit side-chains REVERT: B 14 ASN cc_start: 0.8930 (t0) cc_final: 0.8465 (t0) REVERT: C 14 ASN cc_start: 0.8613 (t0) cc_final: 0.8173 (t0) REVERT: D 14 ASN cc_start: 0.8653 (t0) cc_final: 0.8025 (t0) REVERT: E 14 ASN cc_start: 0.8493 (t0) cc_final: 0.8030 (t0) REVERT: F 14 ASN cc_start: 0.8509 (t0) cc_final: 0.7928 (t0) REVERT: F 26 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8646 (tt) REVERT: I 21 ASN cc_start: 0.6032 (OUTLIER) cc_final: 0.5813 (m-40) outliers start: 23 outliers final: 18 residues processed: 37 average time/residue: 0.0654 time to fit residues: 3.6263 Evaluate side-chains 33 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 13 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 ASN Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 22 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 8.9990 chunk 16 optimal weight: 30.0000 chunk 20 optimal weight: 0.0020 chunk 0 optimal weight: 60.0000 chunk 19 optimal weight: 40.0000 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 overall best weight: 5.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 14 ASN ** 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 = 0.4692 r_free = 0.4692 target = 0.142837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.135598 restraints weight = 9587.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.137584 restraints weight = 5579.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.138992 restraints weight = 3574.285| |-----------------------------------------------------------------------------| r_work (final): 0.4624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2410 Z= 0.133 Angle : 0.854 7.179 3280 Z= 0.464 Chirality : 0.050 0.270 400 Planarity : 0.003 0.014 430 Dihedral : 10.723 28.248 330 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.00 % Favored : 81.00 % Rotamer: Outliers : 6.67 % Allowed : 22.59 % Favored : 70.74 % 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: -4.61 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.010 0.002 PHE J 23 TYR 0.005 0.001 TYR G 37 ARG 0.001 0.000 ARG E 11 =============================================================================== Job complete usr+sys time: 836.28 seconds wall clock time: 16 minutes 14.08 seconds (974.08 seconds total)