Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 17:54:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/10_2023/7ynp_33968_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/10_2023/7ynp_33968.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/10_2023/7ynp_33968_neut_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/10_2023/7ynp_33968_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/10_2023/7ynp_33968_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/10_2023/7ynp_33968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/10_2023/7ynp_33968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/10_2023/7ynp_33968_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynp_33968/10_2023/7ynp_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-1.21rc1-5097/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: 1.70, per 1000 atoms: 0.66 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: 0.93 Conformation dependent library (CDL) restraints added in 405.3 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: 0.36 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: 1.01 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=" C11 IZM D 201 " pdb=" N12 IZM D 201 " ideal model delta sigma weight residual 1.564 1.480 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C11 IZM F 201 " pdb=" N12 IZM F 201 " ideal model delta sigma weight residual 1.564 1.480 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C13 IZM F 201 " pdb=" S17 IZM F 201 " ideal model delta sigma weight residual 1.543 1.608 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C13 IZM D 201 " pdb=" S17 IZM D 201 " ideal model delta sigma weight residual 1.543 1.608 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C10 IZM F 201 " pdb=" S17 IZM F 201 " ideal model delta sigma weight residual 1.516 1.576 -0.060 2.00e-02 2.50e+03 8.99e+00 ... (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=" N14 IZM F 201 " pdb=" C13 IZM F 201 " pdb=" S17 IZM F 201 " ideal model delta sigma weight residual 140.08 124.21 15.87 3.00e+00 1.11e-01 2.80e+01 angle pdb=" N14 IZM D 201 " pdb=" C13 IZM D 201 " pdb=" S17 IZM D 201 " ideal model delta sigma weight residual 140.08 124.26 15.82 3.00e+00 1.11e-01 2.78e+01 angle pdb=" N12 IZM F 201 " pdb=" C13 IZM F 201 " pdb=" N14 IZM F 201 " ideal model delta sigma weight residual 109.87 125.49 -15.62 3.00e+00 1.11e-01 2.71e+01 angle pdb=" C04 IZM F 201 " pdb=" C03 IZM F 201 " pdb=" O02 IZM F 201 " ideal model delta sigma weight residual 104.49 120.11 -15.62 3.00e+00 1.11e-01 2.71e+01 angle pdb=" C04 IZM D 201 " pdb=" C03 IZM D 201 " pdb=" O02 IZM D 201 " ideal model delta sigma weight residual 104.49 120.04 -15.55 3.00e+00 1.11e-01 2.69e+01 ... (remaining 3491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.36: 1230 11.36 - 22.73: 194 22.73 - 34.09: 42 34.09 - 45.45: 18 45.45 - 56.81: 4 Dihedral angle restraints: 1488 sinusoidal: 498 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 1485 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.090 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.290 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.010 ------------------------------------------------------------------------------- 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 : 0.009 0.084 2584 Z= 0.439 Angle : 1.061 15.868 3496 Z= 0.501 Chirality : 0.056 0.161 456 Planarity : 0.003 0.009 428 Dihedral : 13.168 56.812 864 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 *********************** 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 : 0.292 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 1.5477 time to fit residues: 31.8328 Evaluate side-chains 19 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.276 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3792 ------------------------------------------------------------------------------- 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: 2.9990 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 ** 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: 0.7386 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2584 Z= 0.183 Angle : 0.466 2.656 3496 Z= 0.267 Chirality : 0.050 0.122 456 Planarity : 0.002 0.007 428 Dihedral : 6.863 55.861 372 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.88 % Allowed : 10.85 % 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: -3.52 (0.37), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.28), residues: 354 *********************** 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 36 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 26 time to evaluate : 0.279 Fit side-chains outliers start: 10 outliers final: 1 residues processed: 32 average time/residue: 0.9849 time to fit residues: 32.6608 Evaluate side-chains 23 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.291 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0287 time to fit residues: 0.4394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 ** 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: 0.7388 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2584 Z= 0.147 Angle : 0.414 2.664 3496 Z= 0.241 Chirality : 0.050 0.120 456 Planarity : 0.002 0.015 428 Dihedral : 6.006 45.932 372 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.10 % Allowed : 15.50 % Favored : 81.40 % 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: -2.74 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.32), residues: 354 *********************** 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 34 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.278 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 27 average time/residue: 1.2074 time to fit residues: 33.6197 Evaluate side-chains 25 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.278 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3141 time to fit residues: 2.0530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.0040 overall best weight: 1.1396 ------------------------------------------------------------------------------- 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 ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** 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: 0.7352 moved from start: 0.4196 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= 0.091 Angle : 0.343 1.945 3496 Z= 0.202 Chirality : 0.050 0.120 456 Planarity : 0.002 0.011 428 Dihedral : 4.946 35.939 372 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.33 % Allowed : 17.05 % Favored : 80.62 % 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: -2.45 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.32), residues: 354 *********************** 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 27 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.292 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 21 average time/residue: 1.3289 time to fit residues: 28.8012 Evaluate side-chains 22 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.293 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0267 time to fit residues: 0.5574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 0.0070 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 0.3980 overall best weight: 1.8802 ------------------------------------------------------------------------------- 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 ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN E 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2584 Z= 0.139 Angle : 0.397 2.769 3496 Z= 0.233 Chirality : 0.049 0.118 456 Planarity : 0.002 0.010 428 Dihedral : 5.559 38.184 372 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.26 % Allowed : 18.22 % 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: -2.47 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.31), residues: 354 *********************** 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 29 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 18 time to evaluate : 0.274 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 22 average time/residue: 0.9866 time to fit residues: 22.6379 Evaluate side-chains 24 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 15 time to evaluate : 0.273 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 0.2963 time to fit residues: 1.9540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2584 Z= 0.147 Angle : 0.405 2.528 3496 Z= 0.237 Chirality : 0.049 0.118 456 Planarity : 0.002 0.009 428 Dihedral : 5.614 37.948 372 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.65 % Allowed : 20.16 % Favored : 75.19 % 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: -2.45 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.31), residues: 354 *********************** 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 29 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 17 time to evaluate : 0.273 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 24 average time/residue: 0.9544 time to fit residues: 23.8766 Evaluate side-chains 26 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 16 time to evaluate : 0.269 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.0272 time to fit residues: 0.5574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 0.0060 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- 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 B 79 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2584 Z= 0.100 Angle : 0.352 2.334 3496 Z= 0.207 Chirality : 0.049 0.118 456 Planarity : 0.002 0.008 428 Dihedral : 5.001 34.991 372 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.26 % Allowed : 20.16 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.31), residues: 354 *********************** 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: 11 poor density : 15 time to evaluate : 0.284 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 22 average time/residue: 0.9688 time to fit residues: 22.2657 Evaluate side-chains 22 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 13 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.0282 time to fit residues: 0.5198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 0.0970 chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 overall best weight: 2.4184 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2584 Z= 0.173 Angle : 0.432 2.751 3496 Z= 0.253 Chirality : 0.050 0.117 456 Planarity : 0.002 0.008 428 Dihedral : 5.745 38.622 372 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.04 % Allowed : 18.99 % Favored : 75.97 % 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: -2.44 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.31), residues: 354 *********************** 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 32 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 19 time to evaluate : 0.277 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 27 average time/residue: 0.9894 time to fit residues: 27.7346 Evaluate side-chains 31 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 19 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.3293 time to fit residues: 2.1340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 20 optimal weight: 0.0670 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- 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 B 79 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2584 Z= 0.131 Angle : 0.388 2.468 3496 Z= 0.228 Chirality : 0.050 0.119 456 Planarity : 0.002 0.008 428 Dihedral : 5.406 37.345 372 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.26 % Allowed : 20.93 % Favored : 74.81 % 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: -2.39 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.31), residues: 354 *********************** 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 31 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 20 time to evaluate : 0.274 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 27 average time/residue: 1.0400 time to fit residues: 29.0935 Evaluate side-chains 30 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 20 time to evaluate : 0.339 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.0295 time to fit residues: 0.5586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 B 79 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2584 Z= 0.152 Angle : 0.411 2.714 3496 Z= 0.241 Chirality : 0.049 0.118 456 Planarity : 0.002 0.008 428 Dihedral : 5.618 38.337 372 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.26 % Allowed : 20.54 % Favored : 75.19 % 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: -2.45 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.32), residues: 354 ********************** 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 31 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 20 time to evaluate : 0.276 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 27 average time/residue: 1.0043 time to fit residues: 28.1530 Evaluate side-chains 29 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 20 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.0278 time to fit residues: 0.4781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 0.0060 chunk 21 optimal weight: 5.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4859 r_free = 0.4859 target = 0.190139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.155519 restraints weight = 2503.005| |-----------------------------------------------------------------------------| r_work (start): 0.4476 rms_B_bonded: 2.76 r_work: 0.4372 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.008 2584 Z= 0.058 Angle : 0.314 2.024 3496 Z= 0.185 Chirality : 0.050 0.120 456 Planarity : 0.001 0.008 428 Dihedral : 4.342 31.327 372 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.71 % Allowed : 22.48 % Favored : 74.81 % 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: -2.20 (0.43), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.33), residues: 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1384.79 seconds wall clock time: 25 minutes 20.79 seconds (1520.79 seconds total)