Starting phenix.real_space_refine on Sun Mar 10 17:42:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/03_2024/8byn_16329_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/03_2024/8byn_16329.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/03_2024/8byn_16329_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/03_2024/8byn_16329_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/03_2024/8byn_16329_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/03_2024/8byn_16329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/03_2024/8byn_16329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/03_2024/8byn_16329_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/03_2024/8byn_16329_updated.pdb" } resolution = 2.6 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= 0.001 sd= 0.007 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2256 2.51 5 N 654 2.21 5 O 642 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 342": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "F GLU 342": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3564 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'S9C': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'S9C': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'S9C': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'S9C': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.22, per 1000 atoms: 0.62 Number of scatterers: 3564 At special positions: 0 Unit cell: (122.776, 142.552, 43.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 F 6 9.00 O 642 8.00 N 654 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: 1.11 Conformation dependent library (CDL) restraints added in 554.8 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 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: 0.55 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: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1164 1.34 - 1.45: 448 1.45 - 1.57: 2018 1.57 - 1.68: 0 1.68 - 1.80: 6 Bond restraints: 3636 Sorted by residual: bond pdb=" C1 S9C E 501 " pdb=" C3 S9C E 501 " ideal model delta sigma weight residual 1.388 1.510 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C1 S9C A 501 " pdb=" C3 S9C A 501 " ideal model delta sigma weight residual 1.388 1.510 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C1 S9C F 501 " pdb=" C3 S9C F 501 " ideal model delta sigma weight residual 1.388 1.510 -0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C1 S9C F 502 " pdb=" C3 S9C F 502 " ideal model delta sigma weight residual 1.388 1.509 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" C1 S9C B 501 " pdb=" C3 S9C B 501 " ideal model delta sigma weight residual 1.388 1.509 -0.121 2.00e-02 2.50e+03 3.68e+01 ... (remaining 3631 not shown) Histogram of bond angle deviations from ideal: 101.95 - 108.89: 398 108.89 - 115.83: 2063 115.83 - 122.76: 1770 122.76 - 129.70: 599 129.70 - 136.64: 48 Bond angle restraints: 4878 Sorted by residual: angle pdb=" C15 S9C F 502 " pdb=" C16 S9C F 502 " pdb=" F1 S9C F 502 " ideal model delta sigma weight residual 133.16 116.76 16.40 3.00e+00 1.11e-01 2.99e+01 angle pdb=" C15 S9C F 501 " pdb=" C16 S9C F 501 " pdb=" F1 S9C F 501 " ideal model delta sigma weight residual 133.16 116.77 16.39 3.00e+00 1.11e-01 2.99e+01 angle pdb=" C15 S9C E 502 " pdb=" C16 S9C E 502 " pdb=" F1 S9C E 502 " ideal model delta sigma weight residual 133.16 116.77 16.39 3.00e+00 1.11e-01 2.99e+01 angle pdb=" C15 S9C B 501 " pdb=" C16 S9C B 501 " pdb=" F1 S9C B 501 " ideal model delta sigma weight residual 133.16 116.78 16.38 3.00e+00 1.11e-01 2.98e+01 angle pdb=" C15 S9C A 501 " pdb=" C16 S9C A 501 " pdb=" F1 S9C A 501 " ideal model delta sigma weight residual 133.16 116.82 16.34 3.00e+00 1.11e-01 2.97e+01 ... (remaining 4873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 1858 15.91 - 31.83: 194 31.83 - 47.74: 78 47.74 - 63.65: 0 63.65 - 79.56: 6 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" CA ILE E 360 " pdb=" C ILE E 360 " pdb=" N THR E 361 " pdb=" CA THR E 361 " ideal model delta harmonic sigma weight residual 180.00 161.99 18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ILE F 360 " pdb=" C ILE F 360 " pdb=" N THR F 361 " pdb=" CA THR F 361 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ILE B 360 " pdb=" C ILE B 360 " pdb=" N THR B 361 " pdb=" CA THR B 361 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 261 0.026 - 0.051: 140 0.051 - 0.077: 37 0.077 - 0.102: 55 0.102 - 0.128: 35 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA ILE E 328 " pdb=" N ILE E 328 " pdb=" C ILE E 328 " pdb=" CB ILE E 328 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE C 328 " pdb=" N ILE C 328 " pdb=" C ILE C 328 " pdb=" CB ILE C 328 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE B 328 " pdb=" N ILE B 328 " pdb=" C ILE B 328 " pdb=" CB ILE B 328 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 525 not shown) Planarity restraints: 606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 S9C E 502 " 0.001 2.00e-02 2.50e+03 5.96e-03 1.24e+00 pdb=" C10 S9C E 502 " -0.000 2.00e-02 2.50e+03 pdb=" C11 S9C E 502 " -0.016 2.00e-02 2.50e+03 pdb=" C12 S9C E 502 " -0.001 2.00e-02 2.50e+03 pdb=" C2 S9C E 502 " 0.001 2.00e-02 2.50e+03 pdb=" C3 S9C E 502 " 0.001 2.00e-02 2.50e+03 pdb=" C4 S9C E 502 " -0.000 2.00e-02 2.50e+03 pdb=" C5 S9C E 502 " 0.004 2.00e-02 2.50e+03 pdb=" C6 S9C E 502 " 0.014 2.00e-02 2.50e+03 pdb=" C7 S9C E 502 " 0.002 2.00e-02 2.50e+03 pdb=" C8 S9C E 502 " 0.001 2.00e-02 2.50e+03 pdb=" C9 S9C E 502 " -0.004 2.00e-02 2.50e+03 pdb=" N1 S9C E 502 " -0.001 2.00e-02 2.50e+03 pdb=" N2 S9C E 502 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 S9C F 501 " -0.001 2.00e-02 2.50e+03 5.95e-03 1.24e+00 pdb=" C10 S9C F 501 " 0.001 2.00e-02 2.50e+03 pdb=" C11 S9C F 501 " 0.017 2.00e-02 2.50e+03 pdb=" C12 S9C F 501 " 0.001 2.00e-02 2.50e+03 pdb=" C2 S9C F 501 " -0.001 2.00e-02 2.50e+03 pdb=" C3 S9C F 501 " -0.001 2.00e-02 2.50e+03 pdb=" C4 S9C F 501 " 0.000 2.00e-02 2.50e+03 pdb=" C5 S9C F 501 " -0.005 2.00e-02 2.50e+03 pdb=" C6 S9C F 501 " -0.013 2.00e-02 2.50e+03 pdb=" C7 S9C F 501 " -0.001 2.00e-02 2.50e+03 pdb=" C8 S9C F 501 " -0.002 2.00e-02 2.50e+03 pdb=" C9 S9C F 501 " 0.004 2.00e-02 2.50e+03 pdb=" N1 S9C F 501 " 0.000 2.00e-02 2.50e+03 pdb=" N2 S9C F 501 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 S9C E 501 " 0.002 2.00e-02 2.50e+03 5.94e-03 1.24e+00 pdb=" C10 S9C E 501 " -0.001 2.00e-02 2.50e+03 pdb=" C11 S9C E 501 " -0.016 2.00e-02 2.50e+03 pdb=" C12 S9C E 501 " -0.001 2.00e-02 2.50e+03 pdb=" C2 S9C E 501 " 0.001 2.00e-02 2.50e+03 pdb=" C3 S9C E 501 " 0.001 2.00e-02 2.50e+03 pdb=" C4 S9C E 501 " -0.000 2.00e-02 2.50e+03 pdb=" C5 S9C E 501 " 0.004 2.00e-02 2.50e+03 pdb=" C6 S9C E 501 " 0.013 2.00e-02 2.50e+03 pdb=" C7 S9C E 501 " 0.001 2.00e-02 2.50e+03 pdb=" C8 S9C E 501 " 0.002 2.00e-02 2.50e+03 pdb=" C9 S9C E 501 " -0.004 2.00e-02 2.50e+03 pdb=" N1 S9C E 501 " -0.000 2.00e-02 2.50e+03 pdb=" N2 S9C E 501 " -0.001 2.00e-02 2.50e+03 ... (remaining 603 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 1392 2.91 - 3.41: 2717 3.41 - 3.91: 6577 3.91 - 4.40: 6257 4.40 - 4.90: 12280 Nonbonded interactions: 29223 Sorted by model distance: nonbonded pdb=" OD2 ASP F 314 " pdb=" NZ LYS F 370 " model vdw 2.417 2.520 nonbonded pdb=" OD2 ASP E 314 " pdb=" NZ LYS E 370 " model vdw 2.418 2.520 nonbonded pdb=" OD2 ASP C 314 " pdb=" NZ LYS C 370 " model vdw 2.418 2.520 nonbonded pdb=" OD2 ASP D 314 " pdb=" NZ LYS D 370 " model vdw 2.418 2.520 nonbonded pdb=" OD2 ASP B 314 " pdb=" NZ LYS B 370 " model vdw 2.418 2.520 ... (remaining 29218 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 305 through 379) selection = (chain 'B' and resid 305 through 379) selection = chain 'C' selection = chain 'D' selection = (chain 'E' and resid 305 through 379) selection = (chain 'F' and resid 305 through 379) } 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.890 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 12.550 Find NCS groups from input model: 0.230 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:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 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 : 0.010 0.122 3636 Z= 0.497 Angle : 1.133 16.403 4878 Z= 0.500 Chirality : 0.051 0.128 528 Planarity : 0.004 0.022 606 Dihedral : 14.757 79.561 1344 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: -1.93 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 374 PHE 0.006 0.002 PHE B 346 TYR 0.007 0.002 TYR C 310 ARG 0.010 0.003 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.434 Fit side-chains REVERT: D 342 GLU cc_start: 0.7990 (tt0) cc_final: 0.7771 (tt0) REVERT: E 311 LYS cc_start: 0.8492 (mttt) cc_final: 0.8250 (mmtm) REVERT: F 311 LYS cc_start: 0.8401 (mttt) cc_final: 0.8110 (mmtm) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 1.7237 time to fit residues: 250.9471 Evaluate side-chains 83 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3636 Z= 0.163 Angle : 0.501 4.844 4878 Z= 0.256 Chirality : 0.050 0.150 528 Planarity : 0.003 0.025 606 Dihedral : 4.947 16.814 462 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.26 % Allowed : 15.66 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.007 0.001 PHE F 346 TYR 0.009 0.002 TYR A 310 ARG 0.007 0.002 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.401 Fit side-chains REVERT: C 314 ASP cc_start: 0.8571 (t0) cc_final: 0.8334 (t0) outliers start: 5 outliers final: 1 residues processed: 81 average time/residue: 1.6174 time to fit residues: 133.8692 Evaluate side-chains 81 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 351 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3636 Z= 0.178 Angle : 0.505 4.688 4878 Z= 0.260 Chirality : 0.049 0.130 528 Planarity : 0.003 0.029 606 Dihedral : 4.925 16.505 462 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.52 % Allowed : 20.71 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.006 0.001 PHE F 346 TYR 0.009 0.002 TYR A 310 ARG 0.008 0.002 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.454 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 90 average time/residue: 1.6062 time to fit residues: 147.6600 Evaluate side-chains 96 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain F residue 351 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3636 Z= 0.192 Angle : 0.515 4.611 4878 Z= 0.266 Chirality : 0.049 0.131 528 Planarity : 0.004 0.035 606 Dihedral : 4.946 16.563 462 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.78 % Allowed : 19.95 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.007 0.001 PHE F 346 TYR 0.009 0.002 TYR A 310 ARG 0.008 0.002 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.414 Fit side-chains REVERT: D 311 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7129 (pttp) outliers start: 11 outliers final: 4 residues processed: 95 average time/residue: 1.7865 time to fit residues: 173.0258 Evaluate side-chains 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain F residue 351 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3636 Z= 0.179 Angle : 0.505 4.590 4878 Z= 0.260 Chirality : 0.048 0.130 528 Planarity : 0.004 0.038 606 Dihedral : 4.875 16.354 462 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.53 % Allowed : 20.71 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.006 0.001 PHE F 346 TYR 0.009 0.002 TYR A 310 ARG 0.009 0.002 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.425 Fit side-chains REVERT: D 311 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7134 (pttp) outliers start: 10 outliers final: 4 residues processed: 88 average time/residue: 1.6012 time to fit residues: 143.9473 Evaluate side-chains 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain F residue 351 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3636 Z= 0.271 Angle : 0.567 4.686 4878 Z= 0.294 Chirality : 0.049 0.137 528 Planarity : 0.004 0.035 606 Dihedral : 5.165 17.391 462 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.27 % Allowed : 21.46 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.008 0.002 PHE F 346 TYR 0.011 0.003 TYR C 310 ARG 0.010 0.002 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.448 Fit side-chains REVERT: D 311 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7152 (pttp) outliers start: 9 outliers final: 4 residues processed: 89 average time/residue: 1.5530 time to fit residues: 141.3749 Evaluate side-chains 88 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain F residue 351 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 0.3980 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3636 Z= 0.155 Angle : 0.497 4.501 4878 Z= 0.254 Chirality : 0.048 0.130 528 Planarity : 0.004 0.041 606 Dihedral : 4.822 16.648 462 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.77 % Allowed : 21.97 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 329 PHE 0.006 0.001 PHE F 346 TYR 0.008 0.002 TYR A 310 ARG 0.010 0.002 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.572 Fit side-chains REVERT: D 311 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7184 (pttp) outliers start: 7 outliers final: 4 residues processed: 86 average time/residue: 1.6415 time to fit residues: 144.3423 Evaluate side-chains 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain F residue 351 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 35 optimal weight: 0.0020 chunk 37 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 overall best weight: 3.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3636 Z= 0.152 Angle : 0.501 4.963 4878 Z= 0.255 Chirality : 0.048 0.129 528 Planarity : 0.004 0.041 606 Dihedral : 4.774 16.522 462 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.53 % Allowed : 21.21 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 374 PHE 0.005 0.001 PHE F 346 TYR 0.008 0.002 TYR A 310 ARG 0.010 0.002 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.516 Fit side-chains REVERT: D 311 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7275 (pttp) outliers start: 10 outliers final: 4 residues processed: 88 average time/residue: 1.6047 time to fit residues: 144.3335 Evaluate side-chains 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain F residue 351 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 0.0170 chunk 39 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 0.4980 chunk 38 optimal weight: 0.0470 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 overall best weight: 1.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3636 Z= 0.083 Angle : 0.462 5.216 4878 Z= 0.230 Chirality : 0.048 0.122 528 Planarity : 0.004 0.041 606 Dihedral : 4.299 14.441 462 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.77 % Allowed : 22.22 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 374 PHE 0.003 0.001 PHE F 346 TYR 0.006 0.001 TYR E 310 ARG 0.011 0.002 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.464 Fit side-chains REVERT: D 311 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7276 (pttp) outliers start: 7 outliers final: 2 residues processed: 88 average time/residue: 1.5822 time to fit residues: 142.3248 Evaluate side-chains 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 0.0010 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 33 optimal weight: 0.1980 chunk 13 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 overall best weight: 4.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3636 Z= 0.194 Angle : 0.540 5.355 4878 Z= 0.272 Chirality : 0.049 0.131 528 Planarity : 0.004 0.035 606 Dihedral : 4.783 16.400 462 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.26 % Allowed : 22.47 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 PHE 0.007 0.001 PHE F 346 TYR 0.009 0.002 TYR A 310 ARG 0.011 0.002 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.465 Fit side-chains REVERT: D 311 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7292 (pttp) outliers start: 5 outliers final: 1 residues processed: 85 average time/residue: 1.6250 time to fit residues: 141.1352 Evaluate side-chains 84 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain D residue 311 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 0.0060 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.118687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098504 restraints weight = 3725.076| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.28 r_work: 0.3137 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3636 Z= 0.161 Angle : 0.524 5.690 4878 Z= 0.263 Chirality : 0.049 0.129 528 Planarity : 0.004 0.041 606 Dihedral : 4.737 16.093 462 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.26 % Allowed : 22.47 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 PHE 0.005 0.001 PHE F 346 TYR 0.009 0.002 TYR A 310 ARG 0.010 0.002 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2755.13 seconds wall clock time: 49 minutes 22.86 seconds (2962.86 seconds total)