Starting phenix.real_space_refine on Tue Feb 13 04:37:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tas_25783/02_2024/7tas_25783.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tas_25783/02_2024/7tas_25783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tas_25783/02_2024/7tas_25783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tas_25783/02_2024/7tas_25783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tas_25783/02_2024/7tas_25783.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tas_25783/02_2024/7tas_25783.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2014 2.51 5 N 549 2.21 5 O 570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3147 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 904 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 751 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1454 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.32, per 1000 atoms: 0.74 Number of scatterers: 3147 At special positions: 0 Unit cell: (61, 82, 81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 570 8.00 N 549 7.00 C 2014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.15 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.23 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.17 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " BETA1-6 " NAG A 1 " - " FUC A 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN E 343 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 578.6 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 10.6% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.815A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.877A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.559A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.504A pdb=" N TYR E 421 " --> pdb=" O LYS E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.563A pdb=" N HIS H 59 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.550A pdb=" N ALA L 10 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.550A pdb=" N ALA L 10 " --> pdb=" O THR L 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA6, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.531A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.699A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'E' and resid 473 through 474 100 hydrogen bonds defined for protein. 234 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: 0.84 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 911 1.33 - 1.47: 920 1.47 - 1.60: 1382 1.60 - 1.73: 0 1.73 - 1.86: 16 Bond restraints: 3229 Sorted by residual: bond pdb=" N CYS E 391 " pdb=" CA CYS E 391 " ideal model delta sigma weight residual 1.454 1.534 -0.080 1.23e-02 6.61e+03 4.27e+01 bond pdb=" C CYS E 336 " pdb=" O CYS E 336 " ideal model delta sigma weight residual 1.237 1.313 -0.076 1.29e-02 6.01e+03 3.47e+01 bond pdb=" CA ILE L 29 " pdb=" CB ILE L 29 " ideal model delta sigma weight residual 1.544 1.493 0.051 1.17e-02 7.31e+03 1.90e+01 bond pdb=" N CYS E 336 " pdb=" CA CYS E 336 " ideal model delta sigma weight residual 1.454 1.401 0.053 1.29e-02 6.01e+03 1.70e+01 bond pdb=" CA SER L 95 " pdb=" C SER L 95 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.26e-02 6.30e+03 1.20e+01 ... (remaining 3224 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.82: 110 106.82 - 113.66: 1663 113.66 - 120.50: 1395 120.50 - 127.34: 1199 127.34 - 134.18: 34 Bond angle restraints: 4401 Sorted by residual: angle pdb=" C GLN L 6 " pdb=" N PRO L 7 " pdb=" CA PRO L 7 " ideal model delta sigma weight residual 119.66 125.93 -6.27 7.30e-01 1.88e+00 7.38e+01 angle pdb=" C THR E 478 " pdb=" N PRO E 479 " pdb=" CA PRO E 479 " ideal model delta sigma weight residual 119.90 128.33 -8.43 1.05e+00 9.07e-01 6.44e+01 angle pdb=" C PHE E 490 " pdb=" N PRO E 491 " pdb=" CA PRO E 491 " ideal model delta sigma weight residual 119.87 127.54 -7.67 1.04e+00 9.25e-01 5.44e+01 angle pdb=" C VAL L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 120.03 127.01 -6.98 9.90e-01 1.02e+00 4.97e+01 angle pdb=" C ARG L 55 " pdb=" N PRO L 56 " pdb=" CA PRO L 56 " ideal model delta sigma weight residual 120.31 127.17 -6.86 9.80e-01 1.04e+00 4.89e+01 ... (remaining 4396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 1772 15.95 - 31.90: 102 31.90 - 47.84: 20 47.84 - 63.79: 7 63.79 - 79.74: 4 Dihedral angle restraints: 1905 sinusoidal: 720 harmonic: 1185 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 49.70 43.30 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CA SER H 109 " pdb=" C SER H 109 " pdb=" N ASP H 110 " pdb=" CA ASP H 110 " ideal model delta harmonic sigma weight residual -180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" N LYS L 97 " pdb=" C LYS L 97 " pdb=" CA LYS L 97 " pdb=" CB LYS L 97 " ideal model delta harmonic sigma weight residual 122.80 132.21 -9.41 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 1902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 354 0.092 - 0.183: 111 0.183 - 0.275: 14 0.275 - 0.367: 2 0.367 - 0.458: 2 Chirality restraints: 483 Sorted by residual: chirality pdb=" C1 FUC A 3 " pdb=" O6 NAG A 1 " pdb=" C2 FUC A 3 " pdb=" O5 FUC A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" CA CYS E 336 " pdb=" N CYS E 336 " pdb=" C CYS E 336 " pdb=" CB CYS E 336 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA CYS E 391 " pdb=" N CYS E 391 " pdb=" C CYS E 391 " pdb=" CB CYS E 391 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.43e+00 ... (remaining 480 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " 0.207 2.00e-02 2.50e+03 1.75e-01 3.82e+02 pdb=" C7 NAG A 2 " -0.045 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " -0.042 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " -0.283 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.141 2.00e-02 2.50e+03 1.16e-01 1.69e+02 pdb=" C7 NAG A 1 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.105 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.187 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS H 22 " -0.024 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C CYS H 22 " 0.086 2.00e-02 2.50e+03 pdb=" O CYS H 22 " -0.034 2.00e-02 2.50e+03 pdb=" N ALA H 23 " -0.028 2.00e-02 2.50e+03 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 1424 2.94 - 3.43: 2587 3.43 - 3.92: 5073 3.92 - 4.41: 5879 4.41 - 4.90: 9789 Nonbonded interactions: 24752 Sorted by model distance: nonbonded pdb=" O ASP L 93 " pdb=" O LEU L 96 " model vdw 2.452 3.040 nonbonded pdb=" O SER L 68 " pdb=" OG SER L 68 " model vdw 2.453 2.440 nonbonded pdb=" O ILE L 29 " pdb=" C GLY L 30 " model vdw 2.540 3.270 nonbonded pdb=" C ASP E 364 " pdb=" OD1 ASP E 364 " model vdw 2.569 3.270 nonbonded pdb=" OD1 ASP E 364 " pdb=" N SER E 366 " model vdw 2.580 2.520 ... (remaining 24747 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: 6.910 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: 0.010 Extract box with map and model: 26.770 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.020 Find NCS groups from input model: 0.080 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.013 0.080 3229 Z= 0.858 Angle : 1.497 8.429 4401 Z= 1.025 Chirality : 0.089 0.458 483 Planarity : 0.011 0.175 568 Dihedral : 11.333 79.738 1139 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.69 % Allowed : 3.04 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.38), residues: 409 helix: -5.04 (0.23), residues: 32 sheet: 0.13 (0.41), residues: 139 loop : -0.45 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP H 47 HIS 0.006 0.002 HIS H 32 PHE 0.020 0.003 PHE E 497 TYR 0.033 0.005 TYR H 95 ARG 0.002 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.346 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 70 average time/residue: 0.2356 time to fit residues: 18.8201 Evaluate side-chains 54 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 392 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.0020 chunk 11 optimal weight: 0.7980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 HIS H 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3229 Z= 0.216 Angle : 0.624 8.951 4401 Z= 0.325 Chirality : 0.045 0.144 483 Planarity : 0.004 0.031 568 Dihedral : 4.880 29.851 518 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.71 % Favored : 98.04 % Rotamer: Outliers : 2.36 % Allowed : 9.46 % Favored : 88.18 % 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: -0.28 (0.40), residues: 409 helix: -4.23 (0.68), residues: 26 sheet: 0.33 (0.40), residues: 139 loop : 0.09 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.006 0.002 HIS H 35 PHE 0.012 0.001 PHE E 377 TYR 0.012 0.002 TYR H 60 ARG 0.006 0.001 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.368 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 61 average time/residue: 0.2344 time to fit residues: 16.4502 Evaluate side-chains 52 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain E residue 438 SER Chi-restraints excluded: chain E residue 461 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.0670 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3229 Z= 0.179 Angle : 0.557 8.614 4401 Z= 0.283 Chirality : 0.044 0.135 483 Planarity : 0.003 0.031 568 Dihedral : 4.214 20.933 514 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.04 % Allowed : 10.47 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.41), residues: 409 helix: -3.77 (0.64), residues: 32 sheet: 0.48 (0.40), residues: 139 loop : 0.39 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE E 490 TYR 0.010 0.001 TYR H 60 ARG 0.004 0.000 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.345 Fit side-chains REVERT: H 6 GLU cc_start: 0.8139 (mp0) cc_final: 0.7913 (mp0) outliers start: 9 outliers final: 6 residues processed: 61 average time/residue: 0.2308 time to fit residues: 16.1695 Evaluate side-chains 57 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 16 GLN L 39 HIS E 409 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3229 Z= 0.284 Angle : 0.605 8.640 4401 Z= 0.307 Chirality : 0.045 0.141 483 Planarity : 0.004 0.035 568 Dihedral : 4.308 20.330 514 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.04 % Allowed : 11.15 % Favored : 85.81 % 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: 0.00 (0.41), residues: 409 helix: -3.53 (0.76), residues: 32 sheet: 0.69 (0.42), residues: 138 loop : 0.21 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.005 0.002 HIS H 35 PHE 0.012 0.001 PHE E 490 TYR 0.014 0.002 TYR H 60 ARG 0.003 0.001 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.351 Fit side-chains REVERT: H 6 GLU cc_start: 0.8201 (mp0) cc_final: 0.7898 (mp0) outliers start: 9 outliers final: 7 residues processed: 59 average time/residue: 0.2306 time to fit residues: 15.6710 Evaluate side-chains 58 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.0870 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 16 GLN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3229 Z= 0.199 Angle : 0.567 8.760 4401 Z= 0.281 Chirality : 0.044 0.146 483 Planarity : 0.004 0.036 568 Dihedral : 4.187 20.673 514 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.38 % Allowed : 10.47 % Favored : 86.15 % 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: 0.05 (0.41), residues: 409 helix: -3.60 (0.69), residues: 32 sheet: 0.79 (0.43), residues: 138 loop : 0.21 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.001 PHE E 490 TYR 0.010 0.001 TYR E 453 ARG 0.006 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.307 Fit side-chains REVERT: H 6 GLU cc_start: 0.8181 (mp0) cc_final: 0.7941 (mp0) REVERT: H 102 ARG cc_start: 0.8345 (mtm110) cc_final: 0.8045 (mtm110) outliers start: 10 outliers final: 7 residues processed: 57 average time/residue: 0.2337 time to fit residues: 15.2549 Evaluate side-chains 58 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 438 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3229 Z= 0.250 Angle : 0.587 8.685 4401 Z= 0.291 Chirality : 0.044 0.144 483 Planarity : 0.004 0.035 568 Dihedral : 4.222 20.546 514 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.70 % Allowed : 11.15 % Favored : 86.15 % 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: -0.03 (0.41), residues: 409 helix: -3.70 (0.65), residues: 32 sheet: 0.77 (0.43), residues: 138 loop : 0.13 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.008 0.001 PHE E 490 TYR 0.012 0.001 TYR H 60 ARG 0.007 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.342 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 57 average time/residue: 0.2332 time to fit residues: 15.3063 Evaluate side-chains 57 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 438 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3229 Z= 0.357 Angle : 0.637 8.670 4401 Z= 0.320 Chirality : 0.046 0.160 483 Planarity : 0.004 0.035 568 Dihedral : 4.463 21.326 514 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.04 % Allowed : 10.47 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.40), residues: 409 helix: -3.90 (0.64), residues: 27 sheet: 0.60 (0.42), residues: 138 loop : -0.21 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.010 0.001 PHE E 429 TYR 0.014 0.002 TYR H 60 ARG 0.007 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.362 Fit side-chains REVERT: H 102 ARG cc_start: 0.8372 (mtm110) cc_final: 0.8056 (mtm110) outliers start: 9 outliers final: 8 residues processed: 54 average time/residue: 0.2417 time to fit residues: 15.0624 Evaluate side-chains 57 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 438 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8220 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3229 Z= 0.207 Angle : 0.581 8.823 4401 Z= 0.284 Chirality : 0.044 0.159 483 Planarity : 0.003 0.036 568 Dihedral : 4.291 21.025 514 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.70 % Allowed : 11.82 % Favored : 85.47 % 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: -0.23 (0.41), residues: 409 helix: -3.84 (0.67), residues: 26 sheet: 0.68 (0.42), residues: 138 loop : -0.16 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE E 490 TYR 0.010 0.001 TYR E 453 ARG 0.007 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.340 Fit side-chains REVERT: H 13 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.6407 (tm-30) outliers start: 8 outliers final: 7 residues processed: 56 average time/residue: 0.2394 time to fit residues: 15.4559 Evaluate side-chains 58 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8239 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3229 Z= 0.282 Angle : 0.612 8.743 4401 Z= 0.302 Chirality : 0.045 0.158 483 Planarity : 0.004 0.035 568 Dihedral : 4.343 20.993 514 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.04 % Allowed : 11.82 % Favored : 85.14 % 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: -0.32 (0.41), residues: 409 helix: -3.82 (0.67), residues: 27 sheet: 0.58 (0.42), residues: 138 loop : -0.18 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.001 PHE E 490 TYR 0.011 0.002 TYR H 95 ARG 0.007 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.340 Fit side-chains REVERT: H 13 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.6420 (tm-30) REVERT: H 102 ARG cc_start: 0.8361 (mtm110) cc_final: 0.8059 (mtm110) REVERT: E 490 PHE cc_start: 0.7664 (t80) cc_final: 0.7419 (t80) outliers start: 9 outliers final: 8 residues processed: 53 average time/residue: 0.2379 time to fit residues: 14.5951 Evaluate side-chains 57 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 438 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.0570 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.0060 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 overall best weight: 0.4314 ------------------------------------------------------------------------------- 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: 0.8197 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3229 Z= 0.160 Angle : 0.560 8.769 4401 Z= 0.271 Chirality : 0.043 0.164 483 Planarity : 0.003 0.035 568 Dihedral : 4.153 20.511 514 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.03 % Allowed : 12.84 % Favored : 85.14 % 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: -0.17 (0.41), residues: 409 helix: -3.67 (0.73), residues: 26 sheet: 0.67 (0.42), residues: 138 loop : -0.09 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE E 490 TYR 0.009 0.001 TYR E 453 ARG 0.008 0.001 ARG H 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.358 Fit side-chains REVERT: H 13 GLN cc_start: 0.6678 (OUTLIER) cc_final: 0.6345 (tm-30) REVERT: H 102 ARG cc_start: 0.8292 (mtm110) cc_final: 0.7956 (mtm110) outliers start: 6 outliers final: 5 residues processed: 55 average time/residue: 0.2371 time to fit residues: 15.0363 Evaluate side-chains 56 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.103899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.096406 restraints weight = 4872.244| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.84 r_work: 0.3050 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3229 Z= 0.181 Angle : 0.571 8.685 4401 Z= 0.275 Chirality : 0.043 0.159 483 Planarity : 0.003 0.034 568 Dihedral : 4.108 20.807 514 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.03 % Allowed : 12.84 % Favored : 85.14 % 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: -0.15 (0.41), residues: 409 helix: -3.64 (0.74), residues: 26 sheet: 0.63 (0.41), residues: 138 loop : -0.05 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE E 490 TYR 0.016 0.001 TYR L 37 ARG 0.008 0.001 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1570.03 seconds wall clock time: 28 minutes 42.48 seconds (1722.48 seconds total)