Starting phenix.real_space_refine on Thu Dec 7 18:53:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/12_2023/8byn_16329_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/12_2023/8byn_16329.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/12_2023/8byn_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_16329/12_2023/8byn_16329_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/12_2023/8byn_16329_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/12_2023/8byn_16329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/12_2023/8byn_16329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/12_2023/8byn_16329_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/12_2023/8byn_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-1.21rc1-5172/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: 2.33, per 1000 atoms: 0.65 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: 1.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.66 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: 1.17 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: 1.870 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: 5.570 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.280 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.030 ------------------------------------------------------------------------------- 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 : 0.429 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 1.8633 time to fit residues: 271.1429 Evaluate side-chains 96 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.468 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6171 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 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: 0.9980 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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: 0.8889 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3636 Z= 0.142 Angle : 0.487 4.756 4878 Z= 0.248 Chirality : 0.050 0.146 528 Planarity : 0.003 0.029 606 Dihedral : 4.833 16.427 462 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.01 % Allowed : 16.67 % Favored : 82.32 % 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: -1.66 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.006 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 103 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.414 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 99 average time/residue: 1.7439 time to fit residues: 176.0186 Evaluate side-chains 96 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.3343 time to fit residues: 1.9660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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: 0.8910 moved from start: 0.1795 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= 0.154 Angle : 0.484 4.545 4878 Z= 0.249 Chirality : 0.049 0.129 528 Planarity : 0.003 0.031 606 Dihedral : 4.777 16.157 462 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.77 % Allowed : 20.20 % Favored : 78.03 % 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: -1.59 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.005 0.001 PHE F 346 TYR 0.008 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 107 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.453 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 101 average time/residue: 1.7445 time to fit residues: 179.6687 Evaluate side-chains 101 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 1.5333 time to fit residues: 5.2756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.8910 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 : 0.003 0.020 3636 Z= 0.143 Angle : 0.477 4.504 4878 Z= 0.245 Chirality : 0.048 0.128 528 Planarity : 0.003 0.034 606 Dihedral : 4.689 15.883 462 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.10 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: -1.54 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.005 0.001 PHE F 346 TYR 0.008 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 107 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.473 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 100 average time/residue: 1.8000 time to fit residues: 183.4285 Evaluate side-chains 104 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 0.456 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.4234 time to fit residues: 2.0398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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: 0.8917 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3636 Z= 0.165 Angle : 0.490 4.521 4878 Z= 0.252 Chirality : 0.048 0.129 528 Planarity : 0.004 0.039 606 Dihedral : 4.769 16.137 462 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.02 % Allowed : 21.21 % 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: -1.52 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.005 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 110 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.489 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 106 average time/residue: 1.8074 time to fit residues: 195.1945 Evaluate side-chains 108 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.5605 time to fit residues: 3.7783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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: 0.8941 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 3636 Z= 0.303 Angle : 0.587 4.741 4878 Z= 0.303 Chirality : 0.050 0.135 528 Planarity : 0.004 0.036 606 Dihedral : 5.199 17.393 462 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.53 % Allowed : 21.46 % 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: -1.59 (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 0.002 0.001 HIS C 329 PHE 0.007 0.002 PHE F 346 TYR 0.012 0.003 TYR C 310 ARG 0.009 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 117 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 0.490 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 110 average time/residue: 1.7833 time to fit residues: 199.8610 Evaluate side-chains 107 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.1971 time to fit residues: 2.9221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3636 Z= 0.231 Angle : 0.537 4.602 4878 Z= 0.277 Chirality : 0.049 0.132 528 Planarity : 0.004 0.038 606 Dihedral : 5.046 17.035 462 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.52 % Allowed : 22.98 % Favored : 75.51 % 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: -1.59 (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 0.002 0.001 HIS C 329 PHE 0.006 0.001 PHE E 378 TYR 0.011 0.003 TYR A 310 ARG 0.011 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 112 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 0.453 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 108 average time/residue: 1.7682 time to fit residues: 194.5799 Evaluate side-chains 105 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 overall best weight: 3.8386 ------------------------------------------------------------------------------- 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: 0.8921 moved from start: 0.1941 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= 0.178 Angle : 0.512 4.533 4878 Z= 0.262 Chirality : 0.048 0.132 528 Planarity : 0.004 0.041 606 Dihedral : 4.885 16.662 462 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.52 % Allowed : 23.48 % Favored : 75.00 % 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: -1.56 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (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 E 378 TYR 0.009 0.002 TYR E 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 114 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.497 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 112 average time/residue: 1.7578 time to fit residues: 200.6499 Evaluate side-chains 100 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.430 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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: 0.8914 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3636 Z= 0.145 Angle : 0.497 5.112 4878 Z= 0.252 Chirality : 0.048 0.128 528 Planarity : 0.004 0.042 606 Dihedral : 4.739 16.682 462 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.51 % Allowed : 24.49 % Favored : 75.00 % 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: -1.52 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 329 PHE 0.004 0.001 PHE E 378 TYR 0.009 0.002 TYR E 310 ARG 0.010 0.002 ARG D 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 101 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.585 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 101 average time/residue: 1.7097 time to fit residues: 176.0539 Evaluate side-chains 99 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.471 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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: 0.8912 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3636 Z= 0.140 Angle : 0.499 5.571 4878 Z= 0.253 Chirality : 0.048 0.131 528 Planarity : 0.004 0.042 606 Dihedral : 4.695 16.144 462 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.51 % Allowed : 24.75 % Favored : 74.75 % 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: -1.52 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 329 PHE 0.004 0.001 PHE E 378 TYR 0.008 0.002 TYR E 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 101 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.481 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 99 average time/residue: 1.8745 time to fit residues: 189.2965 Evaluate side-chains 100 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.5481 time to fit residues: 2.1519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 0.0870 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 41 optimal weight: 0.4980 overall best weight: 3.3164 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.119401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.099341 restraints weight = 3737.986| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.27 r_work: 0.3155 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 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= 0.157 Angle : 0.509 5.563 4878 Z= 0.259 Chirality : 0.049 0.134 528 Planarity : 0.004 0.043 606 Dihedral : 4.751 16.089 462 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.76 % Allowed : 24.49 % Favored : 74.75 % 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: -1.53 (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 0.001 0.001 HIS F 329 PHE 0.004 0.001 PHE E 378 TYR 0.009 0.002 TYR E 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: 3129.09 seconds wall clock time: 55 minutes 41.66 seconds (3341.66 seconds total)