Starting phenix.real_space_refine on Sun Mar 10 19:28:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/03_2024/8dnx_27583_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/03_2024/8dnx_27583.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/03_2024/8dnx_27583_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/03_2024/8dnx_27583_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/03_2024/8dnx_27583_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/03_2024/8dnx_27583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/03_2024/8dnx_27583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/03_2024/8dnx_27583_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/03_2024/8dnx_27583_trim_updated.pdb" } resolution = 2.98 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= 0.004 sd= 0.030 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 26 5.16 5 C 2834 2.51 5 N 681 2.21 5 O 730 1.98 5 H 20 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4291 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 474 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 251 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "A" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3479 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 87 Unusual residues: {'SZF': 1, 'SZR': 1, 'T09': 1} Classifications: {'peptide': 4, 'undetermined': 3} Link IDs: {'TRANS': 2, None: 4} Not linked: pdbres="T09 D 1 " pdbres="MLE D 2 " Not linked: pdbres="LEU D 3 " pdbres="SZF D 4 " Not linked: pdbres="SZF D 4 " pdbres="LEU D 5 " Not linked: pdbres="MAA D 6 " pdbres="SZR D 7 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'MAA:plan-1': 1, 'MLE:plan-1': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 3.05, per 1000 atoms: 0.71 Number of scatterers: 4291 At special positions: 0 Unit cell: (93.45, 86.1, 84, 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 26 16.00 O 730 8.00 N 681 7.00 C 2834 6.00 H 20 1.00 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 743.8 milliseconds 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 3 sheets defined 68.9% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 30 through 65 Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 70 through 95 Processing helix chain 'A' and resid 6 through 15 Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 28 through 47 Processing helix chain 'A' and resid 63 through 69 removed outlier: 4.649A pdb=" N VAL A 67 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 108 through 134 removed outlier: 3.657A pdb=" N LYS A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 171 removed outlier: 6.224A pdb=" N ALA A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N GLY A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 196 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 242 through 259 Processing helix chain 'A' and resid 289 through 311 Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 341 through 344 No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 358 through 383 Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 409 through 438 Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 444 through 467 Processing sheet with id= A, first strand: chain 'A' and resid 200 through 203 removed outlier: 3.935A pdb=" N THR A 203 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY A 206 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 262 through 265 Processing sheet with id= C, first strand: chain 'A' and resid 267 through 269 289 hydrogen bonds defined for protein. 855 hydrogen bond angles 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: 1.05 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 30 1.23 - 1.37: 1303 1.37 - 1.52: 1611 1.52 - 1.66: 1391 1.66 - 1.81: 43 Bond restraints: 4378 Sorted by residual: bond pdb=" C LEU D 5 " pdb=" N MAA D 6 " ideal model delta sigma weight residual 1.329 1.507 -0.178 1.40e-02 5.10e+03 1.62e+02 bond pdb=" C MLE D 2 " pdb=" N LEU D 3 " ideal model delta sigma weight residual 1.329 1.487 -0.158 1.40e-02 5.10e+03 1.27e+02 bond pdb=" C58 SZR D 7 " pdb=" O60 SZR D 7 " ideal model delta sigma weight residual 1.401 1.190 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C37 SZF D 4 " pdb=" C38 SZF D 4 " ideal model delta sigma weight residual 1.417 1.581 -0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" C33 SZF D 4 " pdb=" C34 SZF D 4 " ideal model delta sigma weight residual 1.421 1.582 -0.161 2.00e-02 2.50e+03 6.47e+01 ... (remaining 4373 not shown) Histogram of bond angle deviations from ideal: 78.95 - 99.01: 4 99.01 - 119.07: 3628 119.07 - 139.13: 2306 139.13 - 159.19: 0 159.19 - 179.25: 1 Bond angle restraints: 5939 Sorted by residual: angle pdb=" C55 SZR D 7 " pdb=" C56 SZR D 7 " pdb=" N57 SZR D 7 " ideal model delta sigma weight residual 120.00 179.25 -59.25 1.00e+00 1.00e+00 3.51e+03 angle pdb="HD12 LEU D 5 " pdb=" CD1 LEU D 5 " pdb="HD13 LEU D 5 " ideal model delta sigma weight residual 110.00 78.95 31.05 3.00e+00 1.11e-01 1.07e+02 angle pdb=" CG LEU D 5 " pdb=" CD1 LEU D 5 " pdb="HD12 LEU D 5 " ideal model delta sigma weight residual 109.00 80.43 28.57 3.00e+00 1.11e-01 9.07e+01 angle pdb="HD11 LEU D 5 " pdb=" CD1 LEU D 5 " pdb="HD13 LEU D 5 " ideal model delta sigma weight residual 110.00 81.44 28.56 3.00e+00 1.11e-01 9.06e+01 angle pdb=" CG LEU D 5 " pdb=" CD1 LEU D 5 " pdb="HD11 LEU D 5 " ideal model delta sigma weight residual 109.00 80.49 28.51 3.00e+00 1.11e-01 9.03e+01 ... (remaining 5934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 2378 17.13 - 34.26: 171 34.26 - 51.39: 25 51.39 - 68.52: 5 68.52 - 85.65: 4 Dihedral angle restraints: 2583 sinusoidal: 1021 harmonic: 1562 Sorted by residual: dihedral pdb=" CA VAL A 14 " pdb=" C VAL A 14 " pdb=" N ILE A 15 " pdb=" CA ILE A 15 " ideal model delta harmonic sigma weight residual 180.00 150.23 29.77 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ILE A 416 " pdb=" C ILE A 416 " pdb=" N ILE A 417 " pdb=" CA ILE A 417 " ideal model delta harmonic sigma weight residual 180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LYS A 171 " pdb=" C LYS A 171 " pdb=" N GLY A 172 " pdb=" CA GLY A 172 " ideal model delta harmonic sigma weight residual 180.00 163.43 16.57 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 2580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 525 0.046 - 0.093: 144 0.093 - 0.139: 17 0.139 - 0.186: 4 0.186 - 0.232: 6 Chirality restraints: 696 Sorted by residual: chirality pdb=" CG LEU D 5 " pdb=" CB LEU D 5 " pdb=" CD1 LEU D 5 " pdb=" CD2 LEU D 5 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CG LEU D 3 " pdb=" CB LEU D 3 " pdb=" CD1 LEU D 3 " pdb=" CD2 LEU D 3 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB ILE A 15 " pdb=" CA ILE A 15 " pdb=" CG1 ILE A 15 " pdb=" CG2 ILE A 15 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 693 not shown) Planarity restraints: 714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 22 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.44e+00 pdb=" C PRO A 22 " -0.032 2.00e-02 2.50e+03 pdb=" O PRO A 22 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 23 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 357 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO A 358 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 358 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 358 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 9 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO B 10 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 10 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 10 " -0.022 5.00e-02 4.00e+02 ... (remaining 711 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 12 2.33 - 2.90: 1726 2.90 - 3.46: 5419 3.46 - 4.03: 8069 4.03 - 4.60: 12334 Nonbonded interactions: 27560 Sorted by model distance: nonbonded pdb=" HG LEU D 5 " pdb="HD11 LEU D 5 " model vdw 1.761 1.952 nonbonded pdb=" HB2 LEU D 3 " pdb="HD23 LEU D 3 " model vdw 2.062 2.440 nonbonded pdb=" HA LEU D 3 " pdb="HD11 LEU D 3 " model vdw 2.100 2.440 nonbonded pdb=" CD2 LEU D 5 " pdb="HD12 LEU D 5 " model vdw 2.116 2.336 nonbonded pdb=" OH TYR A 336 " pdb=" O PRO A 347 " model vdw 2.185 2.200 ... (remaining 27555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.670 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: 0.120 Extract box with map and model: 3.600 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 16.730 Find NCS groups from input model: 0.090 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:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 : 0.008 0.211 4358 Z= 0.570 Angle : 1.002 59.250 5893 Z= 0.832 Chirality : 0.045 0.232 696 Planarity : 0.004 0.044 714 Dihedral : 12.305 85.652 1575 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.44 % Allowed : 0.00 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.37), residues: 533 helix: 2.05 (0.26), residues: 398 sheet: -1.65 (1.17), residues: 22 loop : -1.05 (0.61), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 379 HIS 0.002 0.001 HIS A 360 PHE 0.009 0.001 PHE A 252 TYR 0.007 0.001 TYR A 173 ARG 0.004 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 0.515 Fit side-chains REVERT: B 13 GLN cc_start: 0.7332 (tp-100) cc_final: 0.7058 (tp40) REVERT: B 17 ASP cc_start: 0.7450 (m-30) cc_final: 0.6709 (m-30) REVERT: A 77 MET cc_start: 0.8766 (mmt) cc_final: 0.8503 (mmt) outliers start: 2 outliers final: 0 residues processed: 111 average time/residue: 0.8635 time to fit residues: 100.4333 Evaluate side-chains 59 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.0060 chunk 13 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN A 27 GLN A 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4358 Z= 0.142 Angle : 0.418 4.344 5893 Z= 0.217 Chirality : 0.035 0.123 696 Planarity : 0.003 0.034 714 Dihedral : 3.978 30.528 605 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.17 % Allowed : 14.04 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.38), residues: 533 helix: 2.89 (0.26), residues: 392 sheet: -1.97 (1.09), residues: 22 loop : -0.91 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 379 HIS 0.003 0.001 HIS B 58 PHE 0.007 0.001 PHE B 33 TYR 0.009 0.001 TYR A 336 ARG 0.004 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 0.484 Fit side-chains REVERT: B 13 GLN cc_start: 0.7301 (tp-100) cc_final: 0.7019 (tp40) REVERT: B 17 ASP cc_start: 0.7527 (m-30) cc_final: 0.6703 (m-30) REVERT: A 77 MET cc_start: 0.8732 (mmt) cc_final: 0.8351 (mmt) outliers start: 19 outliers final: 12 residues processed: 77 average time/residue: 0.7624 time to fit residues: 62.2115 Evaluate side-chains 69 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 447 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 0.0060 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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: 0.7863 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4358 Z= 0.126 Angle : 0.386 4.354 5893 Z= 0.197 Chirality : 0.035 0.128 696 Planarity : 0.003 0.029 714 Dihedral : 3.371 24.987 605 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 26.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.82 % Allowed : 14.91 % Favored : 80.26 % 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: 3.39 (0.39), residues: 533 helix: 3.25 (0.26), residues: 397 sheet: -2.24 (1.05), residues: 22 loop : -0.66 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 379 HIS 0.002 0.001 HIS B 58 PHE 0.007 0.001 PHE A 112 TYR 0.007 0.001 TYR A 455 ARG 0.002 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 65 time to evaluate : 0.435 Fit side-chains REVERT: B 13 GLN cc_start: 0.7456 (tp-100) cc_final: 0.7017 (tp40) REVERT: B 17 ASP cc_start: 0.7451 (m-30) cc_final: 0.6632 (m-30) REVERT: A 77 MET cc_start: 0.8571 (mmt) cc_final: 0.8243 (mmt) REVERT: A 166 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8256 (t70) outliers start: 22 outliers final: 10 residues processed: 73 average time/residue: 0.7676 time to fit residues: 59.3878 Evaluate side-chains 68 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 346 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.7949 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4358 Z= 0.202 Angle : 0.442 4.399 5893 Z= 0.225 Chirality : 0.036 0.126 696 Planarity : 0.003 0.028 714 Dihedral : 3.796 27.790 605 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 26.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.92 % Allowed : 14.47 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.38), residues: 533 helix: 3.29 (0.26), residues: 397 sheet: -2.51 (0.99), residues: 22 loop : -0.59 (0.62), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 379 HIS 0.004 0.001 HIS B 58 PHE 0.011 0.001 PHE B 33 TYR 0.011 0.001 TYR A 173 ARG 0.003 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 59 time to evaluate : 0.524 Fit side-chains REVERT: B 13 GLN cc_start: 0.7190 (tp-100) cc_final: 0.6756 (tp40) REVERT: B 17 ASP cc_start: 0.7468 (m-30) cc_final: 0.6688 (m-30) REVERT: B 32 GLU cc_start: 0.8002 (tp30) cc_final: 0.7656 (tp30) REVERT: C 67 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8086 (mmmm) REVERT: A 77 MET cc_start: 0.8468 (mmt) cc_final: 0.8261 (mmt) outliers start: 27 outliers final: 13 residues processed: 71 average time/residue: 0.6919 time to fit residues: 52.3673 Evaluate side-chains 71 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 320 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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: 0.7960 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4358 Z= 0.204 Angle : 0.416 4.377 5893 Z= 0.214 Chirality : 0.036 0.127 696 Planarity : 0.002 0.027 714 Dihedral : 3.531 26.337 605 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 27.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.17 % Allowed : 17.32 % Favored : 78.51 % 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: 3.58 (0.38), residues: 533 helix: 3.40 (0.26), residues: 397 sheet: -2.61 (0.93), residues: 22 loop : -0.54 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.004 0.001 HIS B 58 PHE 0.008 0.001 PHE B 33 TYR 0.009 0.001 TYR A 173 ARG 0.002 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.530 Fit side-chains REVERT: B 13 GLN cc_start: 0.7181 (tp-100) cc_final: 0.6803 (tp40) REVERT: B 17 ASP cc_start: 0.7428 (m-30) cc_final: 0.6677 (m-30) REVERT: B 32 GLU cc_start: 0.7987 (tp30) cc_final: 0.7699 (tp30) REVERT: A 166 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8278 (t70) REVERT: A 389 ASP cc_start: 0.7959 (m-30) cc_final: 0.7687 (m-30) outliers start: 19 outliers final: 11 residues processed: 70 average time/residue: 0.7340 time to fit residues: 54.6553 Evaluate side-chains 71 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 320 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4358 Z= 0.153 Angle : 0.395 4.705 5893 Z= 0.200 Chirality : 0.036 0.134 696 Planarity : 0.002 0.025 714 Dihedral : 3.374 25.317 605 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 28.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.51 % Allowed : 19.30 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.39), residues: 533 helix: 3.55 (0.26), residues: 397 sheet: -2.63 (0.93), residues: 22 loop : -0.44 (0.64), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 379 HIS 0.003 0.001 HIS B 58 PHE 0.006 0.001 PHE B 33 TYR 0.007 0.001 TYR A 455 ARG 0.002 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.515 Fit side-chains REVERT: B 13 GLN cc_start: 0.7184 (tp-100) cc_final: 0.6789 (tp40) REVERT: B 17 ASP cc_start: 0.7424 (m-30) cc_final: 0.6691 (m-30) REVERT: B 32 GLU cc_start: 0.7934 (tp30) cc_final: 0.7668 (tp30) REVERT: A 166 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8270 (t70) REVERT: A 389 ASP cc_start: 0.7948 (m-30) cc_final: 0.7675 (m-30) outliers start: 16 outliers final: 11 residues processed: 68 average time/residue: 0.7487 time to fit residues: 54.1277 Evaluate side-chains 71 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 428 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN A 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4358 Z= 0.210 Angle : 0.423 4.343 5893 Z= 0.217 Chirality : 0.036 0.143 696 Planarity : 0.002 0.025 714 Dihedral : 3.506 26.660 605 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 28.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.95 % Allowed : 19.74 % Favored : 76.32 % 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: 3.71 (0.38), residues: 533 helix: 3.51 (0.25), residues: 397 sheet: -2.69 (0.87), residues: 24 loop : -0.49 (0.64), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.004 0.001 HIS B 58 PHE 0.010 0.001 PHE B 33 TYR 0.009 0.001 TYR A 455 ARG 0.002 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 55 time to evaluate : 0.534 Fit side-chains REVERT: B 13 GLN cc_start: 0.7045 (tp-100) cc_final: 0.6528 (tp40) REVERT: B 16 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8099 (ptmm) REVERT: B 17 ASP cc_start: 0.7420 (m-30) cc_final: 0.6638 (m-30) REVERT: B 32 GLU cc_start: 0.7942 (tp30) cc_final: 0.7692 (tp30) REVERT: A 389 ASP cc_start: 0.7971 (m-30) cc_final: 0.7686 (m-30) outliers start: 18 outliers final: 13 residues processed: 63 average time/residue: 0.7988 time to fit residues: 53.3699 Evaluate side-chains 70 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 428 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4358 Z= 0.170 Angle : 0.403 5.415 5893 Z= 0.203 Chirality : 0.036 0.134 696 Planarity : 0.002 0.024 714 Dihedral : 3.379 25.319 605 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 28.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.29 % Allowed : 20.61 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.90 (0.39), residues: 533 helix: 3.63 (0.26), residues: 397 sheet: -2.57 (0.90), residues: 24 loop : -0.37 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 379 HIS 0.003 0.001 HIS B 58 PHE 0.007 0.001 PHE B 33 TYR 0.007 0.001 TYR A 173 ARG 0.001 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 0.457 Fit side-chains REVERT: B 13 GLN cc_start: 0.7107 (tp-100) cc_final: 0.6662 (tp40) REVERT: B 17 ASP cc_start: 0.7501 (m-30) cc_final: 0.6631 (m-30) REVERT: B 32 GLU cc_start: 0.7923 (tp30) cc_final: 0.7698 (tp30) REVERT: A 389 ASP cc_start: 0.7960 (m-30) cc_final: 0.7677 (m-30) outliers start: 15 outliers final: 13 residues processed: 65 average time/residue: 0.7735 time to fit residues: 53.1665 Evaluate side-chains 70 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 428 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.0270 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4358 Z= 0.194 Angle : 0.419 4.478 5893 Z= 0.211 Chirality : 0.036 0.137 696 Planarity : 0.002 0.024 714 Dihedral : 3.420 26.008 605 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 29.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.07 % Allowed : 21.05 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.38), residues: 533 helix: 3.58 (0.25), residues: 398 sheet: -2.59 (0.90), residues: 24 loop : -0.32 (0.65), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE B 33 TYR 0.008 0.001 TYR A 455 ARG 0.002 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.494 Fit side-chains REVERT: B 13 GLN cc_start: 0.7213 (tp-100) cc_final: 0.6944 (tp40) REVERT: B 17 ASP cc_start: 0.7471 (m-30) cc_final: 0.6590 (m-30) REVERT: B 32 GLU cc_start: 0.7930 (tp30) cc_final: 0.7693 (tp30) REVERT: A 389 ASP cc_start: 0.7962 (m-30) cc_final: 0.7669 (m-30) outliers start: 14 outliers final: 13 residues processed: 65 average time/residue: 0.7513 time to fit residues: 51.9570 Evaluate side-chains 70 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 6 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4358 Z= 0.140 Angle : 0.387 4.486 5893 Z= 0.195 Chirality : 0.036 0.132 696 Planarity : 0.002 0.024 714 Dihedral : 3.273 24.575 605 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 30.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.63 % Allowed : 21.71 % Favored : 75.66 % 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: 4.05 (0.39), residues: 533 helix: 3.71 (0.25), residues: 398 sheet: -2.57 (0.91), residues: 24 loop : -0.20 (0.65), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 379 HIS 0.001 0.001 HIS B 58 PHE 0.006 0.001 PHE B 33 TYR 0.007 0.001 TYR A 455 ARG 0.001 0.000 ARG A 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.522 Fit side-chains REVERT: B 13 GLN cc_start: 0.7217 (tp-100) cc_final: 0.6980 (tp40) REVERT: B 17 ASP cc_start: 0.7469 (m-30) cc_final: 0.6602 (m-30) REVERT: B 32 GLU cc_start: 0.7919 (tp30) cc_final: 0.7710 (tp30) REVERT: A 389 ASP cc_start: 0.7942 (m-30) cc_final: 0.7648 (m-30) outliers start: 12 outliers final: 11 residues processed: 64 average time/residue: 0.8099 time to fit residues: 54.8867 Evaluate side-chains 69 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 428 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.0770 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.113121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.080176 restraints weight = 7738.335| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.85 r_work: 0.3009 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4358 Z= 0.142 Angle : 0.398 5.912 5893 Z= 0.198 Chirality : 0.036 0.134 696 Planarity : 0.002 0.024 714 Dihedral : 3.234 24.613 605 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 29.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.41 % Allowed : 22.37 % Favored : 75.22 % 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: 4.08 (0.39), residues: 533 helix: 3.72 (0.25), residues: 398 sheet: -2.56 (0.90), residues: 24 loop : -0.16 (0.65), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.003 0.001 HIS B 58 PHE 0.006 0.001 PHE B 33 TYR 0.007 0.001 TYR A 455 ARG 0.001 0.000 ARG A 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1798.12 seconds wall clock time: 33 minutes 0.67 seconds (1980.67 seconds total)