Starting phenix.real_space_refine on Sun Mar 10 17:37:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynm_33966/03_2024/7ynm_33966_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynm_33966/03_2024/7ynm_33966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynm_33966/03_2024/7ynm_33966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynm_33966/03_2024/7ynm_33966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynm_33966/03_2024/7ynm_33966_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynm_33966/03_2024/7ynm_33966_neut_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 2256 2.51 5 N 600 2.21 5 O 664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 3528 Number of models: 1 Model: "" Number of chains: 12 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: "G" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "H" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "I" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "J" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'TFX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'TFX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'TFX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'TFX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.05, per 1000 atoms: 0.58 Number of scatterers: 3528 At special positions: 0 Unit cell: (95.45, 105.41, 34.86, 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 8 16.00 O 664 8.00 N 600 7.00 C 2256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 673.3 milliseconds 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 832 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: 0.50 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: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.31: 576 1.31 - 1.40: 728 1.40 - 1.49: 701 1.49 - 1.58: 1539 1.58 - 1.67: 16 Bond restraints: 3560 Sorted by residual: bond pdb=" C5 TFX B 202 " pdb=" C8 TFX B 202 " ideal model delta sigma weight residual 1.435 1.559 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C5 TFX G 202 " pdb=" C8 TFX G 202 " ideal model delta sigma weight residual 1.435 1.559 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C5 TFX H 202 " pdb=" C8 TFX H 202 " ideal model delta sigma weight residual 1.435 1.558 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C5 TFX A 202 " pdb=" C8 TFX A 202 " ideal model delta sigma weight residual 1.435 1.558 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C2 TFX A 201 " pdb=" N2 TFX A 201 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.76e+01 ... (remaining 3555 not shown) Histogram of bond angle deviations from ideal: 99.62 - 107.00: 40 107.00 - 114.39: 2244 114.39 - 121.78: 1595 121.78 - 129.16: 933 129.16 - 136.55: 20 Bond angle restraints: 4832 Sorted by residual: angle pdb=" C5 TFX H 202 " pdb=" C8 TFX H 202 " pdb=" S1 TFX H 202 " ideal model delta sigma weight residual 120.55 131.25 -10.70 3.00e+00 1.11e-01 1.27e+01 angle pdb=" C5 TFX B 202 " pdb=" C8 TFX B 202 " pdb=" S1 TFX B 202 " ideal model delta sigma weight residual 120.55 131.24 -10.69 3.00e+00 1.11e-01 1.27e+01 angle pdb=" C5 TFX A 202 " pdb=" C8 TFX A 202 " pdb=" S1 TFX A 202 " ideal model delta sigma weight residual 120.55 131.22 -10.67 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C5 TFX G 202 " pdb=" C8 TFX G 202 " pdb=" S1 TFX G 202 " ideal model delta sigma weight residual 120.55 131.18 -10.63 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C10 TFX B 202 " pdb=" S1 TFX B 202 " pdb=" C8 TFX B 202 " ideal model delta sigma weight residual 91.28 100.91 -9.63 3.00e+00 1.11e-01 1.03e+01 ... (remaining 4827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 1896 16.52 - 33.04: 64 33.04 - 49.55: 16 49.55 - 66.07: 16 66.07 - 82.59: 16 Dihedral angle restraints: 2008 sinusoidal: 688 harmonic: 1320 Sorted by residual: dihedral pdb=" CA GLY I 93 " pdb=" C GLY I 93 " pdb=" N PHE I 94 " pdb=" CA PHE I 94 " ideal model delta harmonic sigma weight residual 180.00 167.21 12.79 0 5.00e+00 4.00e-02 6.54e+00 dihedral pdb=" CA GLY J 93 " pdb=" C GLY J 93 " pdb=" N PHE J 94 " pdb=" CA PHE J 94 " ideal model delta harmonic sigma weight residual 180.00 167.23 12.77 0 5.00e+00 4.00e-02 6.52e+00 dihedral pdb=" CA GLY C 93 " pdb=" C GLY C 93 " pdb=" N PHE C 94 " pdb=" CA PHE C 94 " ideal model delta harmonic sigma weight residual 180.00 167.23 12.77 0 5.00e+00 4.00e-02 6.52e+00 ... (remaining 2005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 199 0.025 - 0.051: 223 0.051 - 0.076: 63 0.076 - 0.101: 75 0.101 - 0.127: 48 Chirality restraints: 608 Sorted by residual: chirality pdb=" CA VAL J 49 " pdb=" N VAL J 49 " pdb=" C VAL J 49 " pdb=" CB VAL J 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA VAL B 49 " pdb=" N VAL B 49 " pdb=" C VAL B 49 " pdb=" CB VAL B 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 605 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 TFX H 202 " -0.028 2.00e-02 2.50e+03 3.09e-02 1.91e+01 pdb=" C3 TFX H 202 " -0.030 2.00e-02 2.50e+03 pdb=" C4 TFX H 202 " -0.007 2.00e-02 2.50e+03 pdb=" C5 TFX H 202 " -0.001 2.00e-02 2.50e+03 pdb=" C6 TFX H 202 " -0.009 2.00e-02 2.50e+03 pdb=" C7 TFX H 202 " -0.025 2.00e-02 2.50e+03 pdb=" C8 TFX H 202 " 0.037 2.00e-02 2.50e+03 pdb=" N2 TFX H 202 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 TFX G 202 " -0.029 2.00e-02 2.50e+03 3.08e-02 1.90e+01 pdb=" C3 TFX G 202 " -0.029 2.00e-02 2.50e+03 pdb=" C4 TFX G 202 " -0.007 2.00e-02 2.50e+03 pdb=" C5 TFX G 202 " -0.001 2.00e-02 2.50e+03 pdb=" C6 TFX G 202 " -0.008 2.00e-02 2.50e+03 pdb=" C7 TFX G 202 " -0.024 2.00e-02 2.50e+03 pdb=" C8 TFX G 202 " 0.037 2.00e-02 2.50e+03 pdb=" N2 TFX G 202 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 TFX A 202 " -0.028 2.00e-02 2.50e+03 3.07e-02 1.89e+01 pdb=" C3 TFX A 202 " -0.029 2.00e-02 2.50e+03 pdb=" C4 TFX A 202 " -0.007 2.00e-02 2.50e+03 pdb=" C5 TFX A 202 " -0.001 2.00e-02 2.50e+03 pdb=" C6 TFX A 202 " -0.009 2.00e-02 2.50e+03 pdb=" C7 TFX A 202 " -0.024 2.00e-02 2.50e+03 pdb=" C8 TFX A 202 " 0.037 2.00e-02 2.50e+03 pdb=" N2 TFX A 202 " 0.062 2.00e-02 2.50e+03 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 304 2.76 - 3.29: 3359 3.29 - 3.83: 5817 3.83 - 4.36: 6468 4.36 - 4.90: 13187 Nonbonded interactions: 29135 Sorted by model distance: nonbonded pdb=" CE LYS B 80 " pdb=" C16 TFX B 201 " model vdw 2.219 3.860 nonbonded pdb=" CE LYS H 80 " pdb=" C16 TFX H 201 " model vdw 2.219 3.860 nonbonded pdb=" CE LYS A 80 " pdb=" C16 TFX A 201 " model vdw 2.219 3.860 nonbonded pdb=" CE LYS G 80 " pdb=" C16 TFX G 201 " model vdw 2.220 3.860 nonbonded pdb=" CE LYS C 80 " pdb=" C16 TFX G 202 " model vdw 2.255 3.860 ... (remaining 29130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 97) selection = (chain 'B' and resid 37 through 97) selection = chain 'C' selection = chain 'D' selection = (chain 'G' and resid 37 through 97) selection = (chain 'H' and resid 37 through 97) selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.030 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: 9.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.030 Find NCS groups from input model: 0.240 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:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 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 0.124 3560 Z= 0.564 Angle : 0.991 10.697 4832 Z= 0.415 Chirality : 0.055 0.127 608 Planarity : 0.004 0.031 584 Dihedral : 14.588 82.585 1176 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 39.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.34), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS D 50 PHE 0.011 0.003 PHE B 94 TYR 0.007 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.394 Fit side-chains REVERT: H 46 GLU cc_start: 0.5731 (mt-10) cc_final: 0.5422 (tt0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 1.1999 time to fit residues: 103.6159 Evaluate side-chains 38 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3560 Z= 0.115 Angle : 0.558 4.618 4832 Z= 0.289 Chirality : 0.051 0.137 608 Planarity : 0.002 0.009 584 Dihedral : 18.607 89.962 520 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 7.85 % Allowed : 9.88 % Favored : 82.27 % 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: -2.23 (0.39), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS I 50 PHE 0.004 0.001 PHE C 94 TYR 0.008 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 38 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 LYS cc_start: 0.7412 (tttt) cc_final: 0.7142 (mmpt) outliers start: 27 outliers final: 8 residues processed: 51 average time/residue: 1.2891 time to fit residues: 67.7049 Evaluate side-chains 39 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 32 optimal weight: 0.0010 overall best weight: 4.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 3560 Z= 0.328 Angle : 0.809 5.566 4832 Z= 0.428 Chirality : 0.055 0.170 608 Planarity : 0.004 0.014 584 Dihedral : 20.765 89.942 520 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 8.72 % Allowed : 10.17 % Favored : 81.10 % 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 (0.36), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.006 HIS B 50 PHE 0.010 0.003 PHE C 94 TYR 0.011 0.002 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 24 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7694 (mttt) cc_final: 0.6766 (pttp) outliers start: 30 outliers final: 22 residues processed: 51 average time/residue: 1.3462 time to fit residues: 70.6626 Evaluate side-chains 43 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 21 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS C 62 GLN G 62 GLN H 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3560 Z= 0.208 Angle : 0.657 6.325 4832 Z= 0.340 Chirality : 0.052 0.133 608 Planarity : 0.002 0.011 584 Dihedral : 18.984 86.412 520 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 8.14 % Allowed : 12.50 % Favored : 79.36 % 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: -2.31 (0.36), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS H 50 PHE 0.008 0.002 PHE C 94 TYR 0.008 0.002 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 24 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 45 LYS cc_start: 0.7715 (mtmt) cc_final: 0.7502 (mtmm) REVERT: H 57 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6237 (pt0) REVERT: I 45 LYS cc_start: 0.7752 (mtmt) cc_final: 0.7006 (mmtt) REVERT: I 50 HIS cc_start: 0.6824 (p90) cc_final: 0.6615 (p90) outliers start: 28 outliers final: 20 residues processed: 49 average time/residue: 1.3396 time to fit residues: 67.5199 Evaluate side-chains 42 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 21 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.1980 chunk 19 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS C 62 GLN H 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3560 Z= 0.179 Angle : 0.622 6.213 4832 Z= 0.320 Chirality : 0.051 0.130 608 Planarity : 0.002 0.009 584 Dihedral : 18.061 89.819 520 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 7.27 % Allowed : 14.24 % Favored : 78.49 % 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 (0.37), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS H 50 PHE 0.008 0.002 PHE J 94 TYR 0.006 0.002 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 23 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7659 (mttt) cc_final: 0.6689 (pttp) REVERT: H 57 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6260 (pt0) REVERT: H 80 LYS cc_start: 0.8020 (tttt) cc_final: 0.6979 (tptp) outliers start: 25 outliers final: 20 residues processed: 45 average time/residue: 1.2575 time to fit residues: 58.4195 Evaluate side-chains 41 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 20 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 0.0060 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3560 Z= 0.222 Angle : 0.686 6.553 4832 Z= 0.352 Chirality : 0.051 0.131 608 Planarity : 0.002 0.010 584 Dihedral : 16.922 83.213 520 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 6.98 % Allowed : 15.70 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.36), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.005 HIS H 50 PHE 0.009 0.002 PHE J 94 TYR 0.006 0.001 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 23 time to evaluate : 0.363 Fit side-chains REVERT: G 46 GLU cc_start: 0.6024 (mt-10) cc_final: 0.5617 (mt-10) REVERT: H 43 LYS cc_start: 0.7691 (mttt) cc_final: 0.6733 (pttp) REVERT: H 57 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6327 (pt0) REVERT: H 80 LYS cc_start: 0.8058 (tttt) cc_final: 0.7120 (tptp) REVERT: I 45 LYS cc_start: 0.7823 (mtmt) cc_final: 0.7085 (mmmt) outliers start: 24 outliers final: 20 residues processed: 46 average time/residue: 1.2328 time to fit residues: 58.4534 Evaluate side-chains 42 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 21 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3560 Z= 0.100 Angle : 0.511 7.019 4832 Z= 0.264 Chirality : 0.050 0.127 608 Planarity : 0.001 0.009 584 Dihedral : 15.994 89.712 520 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 5.81 % Allowed : 18.31 % Favored : 75.87 % 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: -2.08 (0.39), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS H 50 PHE 0.007 0.002 PHE J 94 TYR 0.003 0.001 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 25 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: C 45 LYS cc_start: 0.7445 (mtmm) cc_final: 0.6698 (mptt) REVERT: H 80 LYS cc_start: 0.7967 (tttt) cc_final: 0.6922 (tptp) REVERT: I 45 LYS cc_start: 0.7734 (mtmt) cc_final: 0.7051 (mmtt) outliers start: 20 outliers final: 16 residues processed: 45 average time/residue: 1.3644 time to fit residues: 63.2087 Evaluate side-chains 33 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 17 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3560 Z= 0.247 Angle : 0.698 7.170 4832 Z= 0.365 Chirality : 0.051 0.129 608 Planarity : 0.002 0.009 584 Dihedral : 15.813 89.834 520 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer: Outliers : 6.40 % Allowed : 18.31 % Favored : 75.29 % 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: -2.34 (0.37), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.005 HIS J 50 PHE 0.010 0.002 PHE J 94 TYR 0.006 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 21 time to evaluate : 0.382 Fit side-chains REVERT: G 46 GLU cc_start: 0.6137 (mt-10) cc_final: 0.5725 (mt-10) REVERT: H 43 LYS cc_start: 0.7676 (mttt) cc_final: 0.6703 (pttp) REVERT: H 80 LYS cc_start: 0.8032 (tttt) cc_final: 0.7152 (tptp) REVERT: I 45 LYS cc_start: 0.7840 (mtmt) cc_final: 0.7100 (mmmt) outliers start: 22 outliers final: 18 residues processed: 41 average time/residue: 1.2651 time to fit residues: 53.5707 Evaluate side-chains 37 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 19 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3560 Z= 0.216 Angle : 0.676 7.378 4832 Z= 0.350 Chirality : 0.051 0.129 608 Planarity : 0.002 0.010 584 Dihedral : 15.048 89.595 520 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 5.81 % Allowed : 18.90 % Favored : 75.29 % 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: -2.38 (0.37), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.005 HIS H 50 PHE 0.009 0.002 PHE J 94 TYR 0.006 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 24 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: C 45 LYS cc_start: 0.7497 (mtmm) cc_final: 0.6700 (mptt) REVERT: D 58 LYS cc_start: 0.6590 (mttt) cc_final: 0.5932 (pmtt) REVERT: G 46 GLU cc_start: 0.6179 (mt-10) cc_final: 0.5785 (mt-10) REVERT: H 43 LYS cc_start: 0.7656 (mttt) cc_final: 0.6671 (pttp) REVERT: H 80 LYS cc_start: 0.8005 (tttt) cc_final: 0.7111 (tptp) REVERT: I 45 LYS cc_start: 0.7828 (mtmt) cc_final: 0.7060 (mmtt) outliers start: 20 outliers final: 17 residues processed: 43 average time/residue: 1.4393 time to fit residues: 63.6247 Evaluate side-chains 38 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 21 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 0.2980 chunk 30 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.0060 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 overall best weight: 1.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3560 Z= 0.117 Angle : 0.556 7.525 4832 Z= 0.287 Chirality : 0.050 0.126 608 Planarity : 0.002 0.021 584 Dihedral : 13.222 87.820 520 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.94 % Allowed : 19.48 % 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: -2.09 (0.39), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS H 50 PHE 0.008 0.002 PHE J 94 TYR 0.003 0.001 TYR C 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 23 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: C 45 LYS cc_start: 0.7431 (mtmm) cc_final: 0.6685 (mptt) REVERT: D 58 LYS cc_start: 0.6467 (mttt) cc_final: 0.5931 (pmtt) REVERT: G 46 GLU cc_start: 0.5950 (mt-10) cc_final: 0.5577 (mt-10) REVERT: H 80 LYS cc_start: 0.7891 (tttt) cc_final: 0.6971 (tptp) REVERT: I 45 LYS cc_start: 0.7717 (mtmt) cc_final: 0.7014 (mmmt) outliers start: 17 outliers final: 16 residues processed: 39 average time/residue: 1.3580 time to fit residues: 54.6588 Evaluate side-chains 36 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 20 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.217268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.194248 restraints weight = 4085.396| |-----------------------------------------------------------------------------| r_work (start): 0.4601 rms_B_bonded: 2.53 r_work: 0.4502 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3560 Z= 0.166 Angle : 0.613 7.299 4832 Z= 0.320 Chirality : 0.050 0.130 608 Planarity : 0.002 0.017 584 Dihedral : 13.041 89.192 520 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 5.23 % Allowed : 18.90 % Favored : 75.87 % 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 (0.38), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS H 50 PHE 0.008 0.002 PHE J 94 TYR 0.004 0.001 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1752.32 seconds wall clock time: 32 minutes 6.50 seconds (1926.50 seconds total)