Starting phenix.real_space_refine on Thu Dec 7 20:30:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/12_2023/8dnx_27583_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/12_2023/8dnx_27583.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/12_2023/8dnx_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_27583/12_2023/8dnx_27583_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/12_2023/8dnx_27583_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/12_2023/8dnx_27583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/12_2023/8dnx_27583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/12_2023/8dnx_27583_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnx_27583/12_2023/8dnx_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'T09:plan-1': 1, 'SZF:plan-2': 1, 'SZR:plan-1': 1, 'MLE:plan-1': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 3.02, per 1000 atoms: 0.70 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: 2.06 Conformation dependent library (CDL) restraints added in 851.7 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: 1.30 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: 1.34 Time building geometry restraints manager: 2.20 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=" C33 SZF D 4 " pdb=" C34 SZF D 4 " ideal model delta sigma weight residual 1.406 1.582 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" C37 SZF D 4 " pdb=" C38 SZF D 4 " ideal model delta sigma weight residual 1.407 1.581 -0.174 2.00e-02 2.50e+03 7.55e+01 bond pdb=" C34 SZF D 4 " pdb=" C35 SZF D 4 " ideal model delta sigma weight residual 1.388 1.514 -0.126 2.00e-02 2.50e+03 3.98e+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="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 angle pdb=" CG LEU D 5 " pdb=" CD1 LEU D 5 " pdb="HD13 LEU D 5 " ideal model delta sigma weight residual 109.00 132.16 -23.16 3.00e+00 1.11e-01 5.96e+01 ... (remaining 5934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 2356 17.13 - 34.26: 181 34.26 - 51.39: 34 51.39 - 68.52: 6 68.52 - 85.65: 6 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: 0.960 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: 3.710 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.760 Find NCS groups from input model: 0.120 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:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.640 ------------------------------------------------------------------------------- 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 0.178 4358 Z= 0.528 Angle : 0.607 9.790 5893 Z= 0.304 Chirality : 0.045 0.232 696 Planarity : 0.004 0.044 714 Dihedral : 13.221 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 : 0.482 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 111 average time/residue: 0.8748 time to fit residues: 101.7194 Evaluate side-chains 59 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6687 ------------------------------------------------------------------------------- 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: 0.8980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7908 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4358 Z= 0.220 Angle : 0.480 4.337 5893 Z= 0.249 Chirality : 0.037 0.123 696 Planarity : 0.003 0.035 714 Dihedral : 6.268 52.791 605 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 24.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.61 % Allowed : 14.25 % Favored : 81.14 % 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: 2.73 (0.38), residues: 533 helix: 2.80 (0.26), residues: 392 sheet: -2.10 (1.05), residues: 22 loop : -0.93 (0.59), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.005 0.001 HIS B 58 PHE 0.011 0.001 PHE B 33 TYR 0.012 0.001 TYR A 455 ARG 0.004 0.000 ARG A 205 *********************** 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 89 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 0.518 Fit side-chains outliers start: 21 outliers final: 9 residues processed: 79 average time/residue: 0.8047 time to fit residues: 67.1482 Evaluate side-chains 69 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.515 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.3082 time to fit residues: 2.0527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 0.0670 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- 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: 0.7927 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4358 Z= 0.178 Angle : 0.417 4.383 5893 Z= 0.214 Chirality : 0.037 0.131 696 Planarity : 0.003 0.030 714 Dihedral : 5.957 58.183 605 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 25.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.48 % Allowed : 15.35 % Favored : 79.17 % 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: 3.11 (0.39), residues: 533 helix: 3.03 (0.26), residues: 397 sheet: -2.34 (1.01), residues: 22 loop : -0.70 (0.63), residues: 114 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 0.009 0.001 PHE B 33 TYR 0.009 0.001 TYR A 173 ARG 0.002 0.000 ARG A 236 *********************** 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 85 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 60 time to evaluate : 0.515 Fit side-chains outliers start: 25 outliers final: 21 residues processed: 75 average time/residue: 0.7500 time to fit residues: 59.6521 Evaluate side-chains 76 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 55 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 8 average time/residue: 0.4373 time to fit residues: 4.5107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7932 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4358 Z= 0.167 Angle : 0.413 4.963 5893 Z= 0.211 Chirality : 0.036 0.123 696 Planarity : 0.003 0.027 714 Dihedral : 5.722 58.036 605 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 27.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.82 % Allowed : 16.89 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.39), residues: 533 helix: 3.18 (0.26), residues: 397 sheet: -2.48 (0.97), residues: 22 loop : -0.61 (0.63), residues: 114 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 0.008 0.001 PHE B 33 TYR 0.011 0.001 TYR A 263 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 80 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 0.474 Fit side-chains outliers start: 22 outliers final: 18 residues processed: 71 average time/residue: 0.7039 time to fit residues: 53.1977 Evaluate side-chains 76 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 58 time to evaluate : 0.524 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 7 average time/residue: 0.3532 time to fit residues: 3.4005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7940 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4358 Z= 0.165 Angle : 0.414 5.221 5893 Z= 0.209 Chirality : 0.036 0.124 696 Planarity : 0.002 0.025 714 Dihedral : 5.562 56.919 605 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 28.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.82 % Allowed : 17.32 % Favored : 77.85 % 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: 3.51 (0.38), residues: 533 helix: 3.35 (0.26), residues: 397 sheet: -2.59 (0.96), residues: 22 loop : -0.62 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.003 0.001 HIS B 58 PHE 0.008 0.001 PHE B 33 TYR 0.008 0.001 TYR A 263 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 84 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.515 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 74 average time/residue: 0.7047 time to fit residues: 55.5132 Evaluate side-chains 74 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.500 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 7 average time/residue: 0.2151 time to fit residues: 2.4092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.0970 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4358 Z= 0.133 Angle : 0.398 5.446 5893 Z= 0.200 Chirality : 0.036 0.125 696 Planarity : 0.002 0.024 714 Dihedral : 5.481 56.916 605 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 28.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.17 % Allowed : 17.54 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.63 (0.38), residues: 533 helix: 3.44 (0.26), residues: 397 sheet: -2.60 (0.95), residues: 22 loop : -0.53 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 379 HIS 0.002 0.001 HIS B 58 PHE 0.006 0.001 PHE B 33 TYR 0.008 0.001 TYR A 263 ARG 0.001 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 80 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 0.553 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 73 average time/residue: 0.7107 time to fit residues: 55.3803 Evaluate side-chains 73 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 6 average time/residue: 0.5675 time to fit residues: 4.2663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 10 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4358 Z= 0.133 Angle : 0.398 5.442 5893 Z= 0.200 Chirality : 0.036 0.125 696 Planarity : 0.002 0.024 714 Dihedral : 5.482 56.915 605 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 31.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.75 % Allowed : 20.18 % Favored : 78.07 % 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: 3.63 (0.38), residues: 533 helix: 3.44 (0.26), residues: 397 sheet: -2.60 (0.95), residues: 22 loop : -0.53 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 379 HIS 0.002 0.001 HIS B 58 PHE 0.006 0.001 PHE B 33 TYR 0.008 0.001 TYR A 263 ARG 0.001 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 68 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.584 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 67 average time/residue: 0.7032 time to fit residues: 50.3318 Evaluate side-chains 68 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.463 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 1 average time/residue: 0.0827 time to fit residues: 0.7300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7933 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4358 Z= 0.135 Angle : 0.397 5.387 5893 Z= 0.199 Chirality : 0.035 0.125 696 Planarity : 0.002 0.024 714 Dihedral : 5.511 56.912 605 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 31.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.75 % Allowed : 20.18 % Favored : 78.07 % 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: 3.63 (0.38), residues: 533 helix: 3.44 (0.26), residues: 397 sheet: -2.61 (0.95), residues: 22 loop : -0.53 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 379 HIS 0.002 0.001 HIS B 58 PHE 0.006 0.001 PHE B 33 TYR 0.008 0.001 TYR A 263 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 68 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.514 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 67 average time/residue: 0.7021 time to fit residues: 50.2270 Evaluate side-chains 68 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.506 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 1 average time/residue: 0.0830 time to fit residues: 0.7962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4358 Z= 0.241 Angle : 0.472 6.418 5893 Z= 0.237 Chirality : 0.037 0.126 696 Planarity : 0.003 0.024 714 Dihedral : 5.523 52.080 605 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 29.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.07 % Allowed : 19.08 % Favored : 77.85 % 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: 3.31 (0.25), residues: 397 sheet: -2.63 (0.94), residues: 22 loop : -0.62 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.004 0.001 HIS B 58 PHE 0.011 0.001 PHE B 33 TYR 0.010 0.001 TYR A 455 ARG 0.003 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 76 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.575 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 70 average time/residue: 0.7414 time to fit residues: 55.2524 Evaluate side-chains 70 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.462 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 3 average time/residue: 0.1302 time to fit residues: 1.1820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 6 optimal weight: 0.0060 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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: 0.7966 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4358 Z= 0.150 Angle : 0.446 5.838 5893 Z= 0.221 Chirality : 0.036 0.127 696 Planarity : 0.002 0.024 714 Dihedral : 5.521 52.208 605 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 29.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.97 % Allowed : 20.61 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.38), residues: 533 helix: 3.36 (0.25), residues: 397 sheet: -2.62 (0.95), residues: 22 loop : -0.56 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.003 0.001 HIS B 58 PHE 0.011 0.001 PHE B 33 TYR 0.009 0.001 TYR A 455 ARG 0.001 0.000 ARG A 411 ********************** 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 69 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.528 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 67 average time/residue: 0.7009 time to fit residues: 50.1568 Evaluate side-chains 68 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.506 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 2 average time/residue: 0.1338 time to fit residues: 1.0074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 34 optimal weight: 0.0670 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.111994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.079105 restraints weight = 7788.033| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.82 r_work: 0.2993 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4358 Z= 0.150 Angle : 0.446 5.838 5893 Z= 0.221 Chirality : 0.036 0.127 696 Planarity : 0.002 0.024 714 Dihedral : 5.521 52.208 605 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 31.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.75 % Allowed : 21.27 % Favored : 76.97 % 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: 3.52 (0.38), residues: 533 helix: 3.36 (0.25), residues: 397 sheet: -2.62 (0.95), residues: 22 loop : -0.56 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.003 0.001 HIS B 58 PHE 0.011 0.001 PHE B 33 TYR 0.009 0.001 TYR A 455 ARG 0.001 0.000 ARG A 411 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1784.90 seconds wall clock time: 32 minutes 31.38 seconds (1951.38 seconds total)