Starting phenix.real_space_refine on Sun Mar 10 15:08:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/03_2024/7ynp_33968_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/03_2024/7ynp_33968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/03_2024/7ynp_33968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/03_2024/7ynp_33968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/03_2024/7ynp_33968_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/03_2024/7ynp_33968_neut_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 2 5.16 5 C 1620 2.51 5 N 444 2.21 5 O 502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 46": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" 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: 2568 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "B" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "C" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "E" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "F" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'IZM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'IZM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.76, per 1000 atoms: 0.69 Number of scatterers: 2568 At special positions: 0 Unit cell: (97.11, 105.41, 31.54, 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 2 16.00 O 502 8.00 N 444 7.00 C 1620 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: 0.92 Conformation dependent library (CDL) restraints added in 484.7 milliseconds 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 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: 0.33 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: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.30: 432 1.30 - 1.37: 424 1.37 - 1.45: 260 1.45 - 1.53: 1331 1.53 - 1.61: 137 Bond restraints: 2584 Sorted by residual: bond pdb=" C10 IZM D 201 " pdb=" S17 IZM D 201 " ideal model delta sigma weight residual 1.748 1.575 0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" C10 IZM F 201 " pdb=" S17 IZM F 201 " ideal model delta sigma weight residual 1.748 1.576 0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" C09 IZM D 201 " pdb=" C10 IZM D 201 " ideal model delta sigma weight residual 1.433 1.574 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C09 IZM F 201 " pdb=" C10 IZM F 201 " ideal model delta sigma weight residual 1.433 1.573 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C13 IZM D 201 " pdb=" S17 IZM D 201 " ideal model delta sigma weight residual 1.744 1.608 0.136 2.00e-02 2.50e+03 4.60e+01 ... (remaining 2579 not shown) Histogram of bond angle deviations from ideal: 99.25 - 106.30: 10 106.30 - 113.36: 1624 113.36 - 120.41: 851 120.41 - 127.46: 1001 127.46 - 134.52: 10 Bond angle restraints: 3496 Sorted by residual: angle pdb=" C08 IZM F 201 " pdb=" C09 IZM F 201 " pdb=" C10 IZM F 201 " ideal model delta sigma weight residual 125.57 112.89 12.68 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C08 IZM D 201 " pdb=" C09 IZM D 201 " pdb=" C10 IZM D 201 " ideal model delta sigma weight residual 125.57 112.97 12.60 3.00e+00 1.11e-01 1.76e+01 angle pdb=" C07 IZM F 201 " pdb=" C08 IZM F 201 " pdb=" C09 IZM F 201 " ideal model delta sigma weight residual 123.72 111.56 12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" C07 IZM D 201 " pdb=" C08 IZM D 201 " pdb=" C09 IZM D 201 " ideal model delta sigma weight residual 123.72 111.57 12.15 3.00e+00 1.11e-01 1.64e+01 angle pdb=" C10 IZM F 201 " pdb=" S17 IZM F 201 " pdb=" C13 IZM F 201 " ideal model delta sigma weight residual 89.24 99.25 -10.01 3.00e+00 1.11e-01 1.11e+01 ... (remaining 3491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 1322 16.28 - 32.57: 138 32.57 - 48.85: 30 48.85 - 65.13: 0 65.13 - 81.42: 4 Dihedral angle restraints: 1494 sinusoidal: 504 harmonic: 990 Sorted by residual: dihedral pdb=" CB LYS D 60 " pdb=" CG LYS D 60 " pdb=" CD LYS D 60 " pdb=" CE LYS D 60 " ideal model delta sinusoidal sigma weight residual 180.00 140.70 39.30 3 1.50e+01 4.44e-03 6.96e+00 dihedral pdb=" CB LYS B 60 " pdb=" CG LYS B 60 " pdb=" CD LYS B 60 " pdb=" CE LYS B 60 " ideal model delta sinusoidal sigma weight residual 180.00 140.77 39.23 3 1.50e+01 4.44e-03 6.94e+00 dihedral pdb=" CB LYS A 60 " pdb=" CG LYS A 60 " pdb=" CD LYS A 60 " pdb=" CE LYS A 60 " ideal model delta sinusoidal sigma weight residual 180.00 140.78 39.22 3 1.50e+01 4.44e-03 6.94e+00 ... (remaining 1491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 210 0.032 - 0.064: 134 0.064 - 0.097: 52 0.097 - 0.129: 54 0.129 - 0.161: 6 Chirality restraints: 456 Sorted by residual: chirality pdb=" CB THR D 72 " pdb=" CA THR D 72 " pdb=" OG1 THR D 72 " pdb=" CG2 THR D 72 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CB THR A 72 " pdb=" CA THR A 72 " pdb=" OG1 THR A 72 " pdb=" CG2 THR A 72 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CB THR E 72 " pdb=" CA THR E 72 " pdb=" OG1 THR E 72 " pdb=" CG2 THR E 72 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 453 not shown) Planarity restraints: 428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 50 " 0.009 2.00e-02 2.50e+03 8.58e-03 1.10e+00 pdb=" CG HIS A 50 " -0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 50 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS A 50 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 50 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 50 " -0.009 2.00e-02 2.50e+03 8.28e-03 1.03e+00 pdb=" CG HIS F 50 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS F 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS F 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS F 50 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS F 50 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 50 " -0.009 2.00e-02 2.50e+03 8.24e-03 1.02e+00 pdb=" CG HIS E 50 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS E 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 50 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS E 50 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS E 50 " -0.002 2.00e-02 2.50e+03 ... (remaining 425 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 556 2.79 - 3.32: 2112 3.32 - 3.85: 4028 3.85 - 4.37: 4471 4.37 - 4.90: 9061 Nonbonded interactions: 20228 Sorted by model distance: nonbonded pdb=" OE1 GLU D 46 " pdb=" NZ LYS D 80 " model vdw 2.265 2.520 nonbonded pdb=" OE1 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.266 2.520 nonbonded pdb=" OE1 GLU F 46 " pdb=" NZ LYS F 80 " model vdw 2.266 2.520 nonbonded pdb=" OE1 GLU C 46 " pdb=" NZ LYS C 80 " model vdw 2.266 2.520 nonbonded pdb=" OE1 GLU A 46 " pdb=" NZ LYS A 80 " model vdw 2.266 2.520 ... (remaining 20223 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' and resid 37 through 97) selection = chain 'E' selection = (chain 'F' and resid 37 through 97) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 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: 9.090 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.160 Find NCS groups from input model: 0.170 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:11.720 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 : 0.012 0.173 2584 Z= 0.603 Angle : 0.965 12.679 3496 Z= 0.479 Chirality : 0.056 0.161 456 Planarity : 0.003 0.009 428 Dihedral : 13.694 81.418 870 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % 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: -3.88 (0.34), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.26), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.005 HIS A 50 PHE 0.012 0.004 PHE D 94 TYR 0.011 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.291 Fit side-chains REVERT: A 62 GLN cc_start: 0.6485 (tt0) cc_final: 0.6228 (tt0) REVERT: C 62 GLN cc_start: 0.6515 (tt0) cc_final: 0.6287 (tt0) REVERT: D 62 GLN cc_start: 0.6468 (tt0) cc_final: 0.6140 (tt0) REVERT: F 62 GLN cc_start: 0.6465 (tt0) cc_final: 0.6229 (tt0) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 1.4949 time to fit residues: 30.7507 Evaluate side-chains 19 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN B 79 GLN E 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2584 Z= 0.096 Angle : 0.381 2.498 3496 Z= 0.216 Chirality : 0.051 0.123 456 Planarity : 0.001 0.006 428 Dihedral : 4.805 33.622 378 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.71 % Allowed : 6.20 % Favored : 91.09 % 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: -3.25 (0.38), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.006 0.001 PHE E 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 19 time to evaluate : 0.364 Fit side-chains REVERT: A 62 GLN cc_start: 0.6612 (tt0) cc_final: 0.6401 (tt0) REVERT: A 79 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: B 62 GLN cc_start: 0.7212 (tt0) cc_final: 0.7002 (tt0) REVERT: C 62 GLN cc_start: 0.6629 (tt0) cc_final: 0.6382 (tm-30) outliers start: 7 outliers final: 0 residues processed: 25 average time/residue: 1.0340 time to fit residues: 26.7803 Evaluate side-chains 19 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.0010 chunk 10 optimal weight: 8.9990 chunk 27 optimal weight: 0.0060 chunk 22 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 35 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 overall best weight: 0.8204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 79 GLN B 65 ASN C 65 ASN E 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2584 Z= 0.082 Angle : 0.335 2.647 3496 Z= 0.197 Chirality : 0.050 0.117 456 Planarity : 0.002 0.014 428 Dihedral : 3.230 11.150 378 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.39 % Allowed : 12.40 % Favored : 87.21 % 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: -2.27 (0.43), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 50 PHE 0.006 0.001 PHE F 94 TYR 0.004 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.242 Fit side-chains REVERT: A 79 GLN cc_start: 0.7876 (pt0) cc_final: 0.7172 (tt0) REVERT: D 79 GLN cc_start: 0.7925 (pt0) cc_final: 0.7669 (tt0) REVERT: F 79 GLN cc_start: 0.7929 (pt0) cc_final: 0.7438 (tt0) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 1.4332 time to fit residues: 28.0466 Evaluate side-chains 18 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN C 65 ASN E 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2584 Z= 0.100 Angle : 0.338 2.223 3496 Z= 0.201 Chirality : 0.049 0.117 456 Planarity : 0.002 0.011 428 Dihedral : 3.496 10.676 378 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.94 % Allowed : 12.79 % Favored : 85.27 % 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: -1.99 (0.43), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.007 0.002 PHE B 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.306 Fit side-chains REVERT: A 79 GLN cc_start: 0.7869 (pt0) cc_final: 0.7350 (tt0) REVERT: B 79 GLN cc_start: 0.7774 (pt0) cc_final: 0.7408 (tt0) REVERT: D 62 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6578 (tm-30) REVERT: F 79 GLN cc_start: 0.7861 (pt0) cc_final: 0.7409 (tt0) outliers start: 5 outliers final: 2 residues processed: 23 average time/residue: 1.3837 time to fit residues: 32.7824 Evaluate side-chains 19 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 62 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 20.0000 chunk 25 optimal weight: 0.3980 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 0.1980 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.0060 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN C 65 ASN E 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2584 Z= 0.101 Angle : 0.336 2.368 3496 Z= 0.201 Chirality : 0.049 0.119 456 Planarity : 0.002 0.010 428 Dihedral : 3.311 10.103 378 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.33 % Allowed : 12.79 % Favored : 84.88 % 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: -1.91 (0.43), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 50 PHE 0.005 0.001 PHE B 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.245 Fit side-chains REVERT: A 79 GLN cc_start: 0.7738 (pt0) cc_final: 0.7335 (tt0) REVERT: B 79 GLN cc_start: 0.7807 (pt0) cc_final: 0.7481 (tt0) REVERT: D 62 GLN cc_start: 0.6849 (OUTLIER) cc_final: 0.6561 (tm-30) REVERT: F 79 GLN cc_start: 0.7823 (pt0) cc_final: 0.7443 (tt0) outliers start: 6 outliers final: 3 residues processed: 19 average time/residue: 1.4725 time to fit residues: 28.7702 Evaluate side-chains 21 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 17 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2584 Z= 0.213 Angle : 0.479 3.433 3496 Z= 0.281 Chirality : 0.050 0.118 456 Planarity : 0.003 0.008 428 Dihedral : 4.417 12.965 378 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.65 % Allowed : 12.79 % Favored : 82.56 % 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: -2.21 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS A 50 PHE 0.006 0.002 PHE B 94 TYR 0.007 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 20 time to evaluate : 0.249 Fit side-chains REVERT: D 62 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6655 (tm-30) REVERT: F 79 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7430 (tt0) outliers start: 12 outliers final: 7 residues processed: 24 average time/residue: 1.2390 time to fit residues: 30.6587 Evaluate side-chains 28 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 19 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 79 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN C 65 ASN E 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2584 Z= 0.104 Angle : 0.350 2.457 3496 Z= 0.209 Chirality : 0.049 0.120 456 Planarity : 0.001 0.009 428 Dihedral : 3.570 11.148 378 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.10 % Allowed : 17.83 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.004 0.001 PHE B 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 18 time to evaluate : 0.263 Fit side-chains REVERT: A 79 GLN cc_start: 0.7667 (pt0) cc_final: 0.7365 (tt0) REVERT: D 62 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6628 (tm-30) REVERT: F 79 GLN cc_start: 0.7816 (pt0) cc_final: 0.7476 (tt0) outliers start: 8 outliers final: 6 residues processed: 21 average time/residue: 1.2468 time to fit residues: 27.0406 Evaluate side-chains 25 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 18 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 0.0070 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 0.0040 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 65 ASN C 65 ASN E 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 2584 Z= 0.065 Angle : 0.304 2.272 3496 Z= 0.182 Chirality : 0.049 0.118 456 Planarity : 0.001 0.008 428 Dihedral : 2.980 8.876 378 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.49 % Allowed : 17.83 % Favored : 78.68 % 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: -1.88 (0.43), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.004 0.001 PHE B 94 TYR 0.004 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 18 time to evaluate : 0.273 Fit side-chains REVERT: A 79 GLN cc_start: 0.7644 (pt0) cc_final: 0.7386 (tt0) REVERT: D 62 GLN cc_start: 0.6860 (OUTLIER) cc_final: 0.6588 (tm-30) REVERT: F 79 GLN cc_start: 0.7795 (pt0) cc_final: 0.7486 (tt0) REVERT: F 83 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6963 (mt-10) outliers start: 9 outliers final: 7 residues processed: 22 average time/residue: 1.3529 time to fit residues: 30.6533 Evaluate side-chains 27 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 18 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 83 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2584 Z= 0.235 Angle : 0.499 3.331 3496 Z= 0.292 Chirality : 0.050 0.118 456 Planarity : 0.003 0.009 428 Dihedral : 4.413 14.228 378 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 6.20 % Allowed : 16.28 % Favored : 77.52 % 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: -2.18 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.006 HIS A 50 PHE 0.006 0.002 PHE E 94 TYR 0.006 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 21 time to evaluate : 0.271 Fit side-chains REVERT: D 62 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6685 (tm-30) REVERT: F 79 GLN cc_start: 0.7850 (pt0) cc_final: 0.7426 (tt0) outliers start: 16 outliers final: 11 residues processed: 29 average time/residue: 1.0409 time to fit residues: 31.2317 Evaluate side-chains 33 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 21 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 8.9990 chunk 22 optimal weight: 0.0170 chunk 17 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 0.2980 overall best weight: 2.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN E 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2584 Z= 0.161 Angle : 0.416 2.764 3496 Z= 0.244 Chirality : 0.049 0.121 456 Planarity : 0.002 0.008 428 Dihedral : 4.043 13.601 378 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.65 % Allowed : 17.83 % Favored : 77.52 % 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: -2.23 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS A 50 PHE 0.005 0.001 PHE E 94 TYR 0.006 0.001 TYR C 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 20 time to evaluate : 0.270 Fit side-chains REVERT: A 79 GLN cc_start: 0.7667 (pt0) cc_final: 0.7317 (tt0) REVERT: D 62 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6681 (tm-30) REVERT: F 79 GLN cc_start: 0.7808 (pt0) cc_final: 0.7440 (tt0) outliers start: 12 outliers final: 11 residues processed: 27 average time/residue: 1.1846 time to fit residues: 32.9981 Evaluate side-chains 32 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 20 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN E 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.188112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.150599 restraints weight = 2515.069| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 2.84 r_work: 0.4309 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.4163 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2584 Z= 0.244 Angle : 0.516 3.495 3496 Z= 0.300 Chirality : 0.050 0.119 456 Planarity : 0.003 0.009 428 Dihedral : 4.712 14.951 378 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.04 % Allowed : 17.44 % Favored : 77.52 % 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: -2.51 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.006 HIS A 50 PHE 0.006 0.002 PHE E 94 TYR 0.006 0.002 TYR C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1385.34 seconds wall clock time: 25 minutes 14.14 seconds (1514.14 seconds total)