Starting phenix.real_space_refine on Fri Aug 2 12:30:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoa_42432/08_2024/8uoa_42432_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoa_42432/08_2024/8uoa_42432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoa_42432/08_2024/8uoa_42432.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoa_42432/08_2024/8uoa_42432.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoa_42432/08_2024/8uoa_42432_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoa_42432/08_2024/8uoa_42432_neut.cif" } resolution = 3.8 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= 0.013 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 2 5.16 5 C 888 2.51 5 N 251 2.21 5 O 299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 560": "OD1" <-> "OD2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 1440 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 1, 'TRANS': 94} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 587 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 4, 'TRANS': 114} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 188 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.26, per 1000 atoms: 1.57 Number of scatterers: 1440 At special positions: 0 Unit cell: (59.616, 57.672, 68.688, 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 2 16.00 O 299 8.00 N 251 7.00 C 888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG C 1 " - " ASN A 573 " " NAG D 1 " - " ASN A 548 " " NAG E 1 " - " ASN A 498 " Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 319.7 milliseconds 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 396 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 6 sheets defined 3.3% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing sheet with id=AA1, first strand: chain 'A' and resid 515 through 516 Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 532 removed outlier: 5.786A pdb=" N PHE A 526 " --> pdb=" O ARG A 547 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N CYS A 549 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP A 528 " --> pdb=" O CYS A 549 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N PHE A 551 " --> pdb=" O ASP A 528 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N LEU A 530 " --> pdb=" O PHE A 551 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N ASN A 553 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU A 532 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N VAL A 555 " --> pdb=" O GLU A 532 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N LEU A 571 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N THR A 550 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N ASN A 573 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE A 552 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N THR A 575 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR A 554 " --> pdb=" O THR A 575 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 558 through 559 removed outlier: 3.681A pdb=" N THR A 559 " --> pdb=" O HIS A 578 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.155A pdb=" N VAL B 98 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL B 33 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N MET B 34 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 47 hydrogen bonds defined for protein. 105 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: 0.35 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 323 1.33 - 1.45: 362 1.45 - 1.57: 771 1.57 - 1.69: 0 1.69 - 1.81: 2 Bond restraints: 1458 Sorted by residual: bond pdb=" N VAL B 63 " pdb=" CA VAL B 63 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.09e-02 8.42e+03 1.16e+01 bond pdb=" CA LEU B 85 " pdb=" C LEU B 85 " ideal model delta sigma weight residual 1.526 1.487 0.039 1.20e-02 6.94e+03 1.05e+01 bond pdb=" CA MET B 82 " pdb=" C MET B 82 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.24e-02 6.50e+03 8.95e+00 bond pdb=" CA LEU B 80 " pdb=" C LEU B 80 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.23e-02 6.61e+03 7.95e+00 bond pdb=" C VAL B 12 " pdb=" O VAL B 12 " ideal model delta sigma weight residual 1.236 1.208 0.028 9.90e-03 1.02e+04 7.79e+00 ... (remaining 1453 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.19: 9 105.19 - 111.70: 692 111.70 - 118.21: 430 118.21 - 124.73: 830 124.73 - 131.24: 30 Bond angle restraints: 1991 Sorted by residual: angle pdb=" N ARG B 32 " pdb=" CA ARG B 32 " pdb=" C ARG B 32 " ideal model delta sigma weight residual 108.67 98.68 9.99 1.55e+00 4.16e-01 4.16e+01 angle pdb=" C LYS B 86 " pdb=" N PRO B 87 " pdb=" CA PRO B 87 " ideal model delta sigma weight residual 119.47 126.72 -7.25 1.16e+00 7.43e-01 3.90e+01 angle pdb=" N THR B 101 " pdb=" CA THR B 101 " pdb=" C THR B 101 " ideal model delta sigma weight residual 110.19 117.85 -7.66 1.24e+00 6.50e-01 3.82e+01 angle pdb=" N ALA B 52 " pdb=" CA ALA B 52 " pdb=" C ALA B 52 " ideal model delta sigma weight residual 111.71 118.09 -6.38 1.15e+00 7.56e-01 3.08e+01 angle pdb=" C GLY B 104 " pdb=" N PRO B 105 " pdb=" CA PRO B 105 " ideal model delta sigma weight residual 119.76 125.47 -5.71 1.03e+00 9.43e-01 3.08e+01 ... (remaining 1986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.00: 847 21.00 - 41.99: 41 41.99 - 62.99: 15 62.99 - 83.98: 7 83.98 - 104.98: 13 Dihedral angle restraints: 923 sinusoidal: 310 harmonic: 613 Sorted by residual: dihedral pdb=" CA LEU A 521 " pdb=" C LEU A 521 " pdb=" N LYS A 522 " pdb=" CA LYS A 522 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" C1 NAG C 2 " pdb=" C2 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" O3 NAG C 2 " ideal model delta sinusoidal sigma weight residual -175.09 -70.11 -104.98 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" C2 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" C4 NAG C 2 " pdb=" O4 NAG C 2 " ideal model delta sinusoidal sigma weight residual 175.11 70.32 104.79 1 3.00e+01 1.11e-03 1.34e+01 ... (remaining 920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 214 0.092 - 0.184: 34 0.184 - 0.276: 5 0.276 - 0.369: 1 0.369 - 0.461: 2 Chirality restraints: 256 Sorted by residual: chirality pdb=" C5 NAG E 2 " pdb=" C4 NAG E 2 " pdb=" C6 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.41 -1.95 -0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.88e+00 chirality pdb=" C4 NAG E 2 " pdb=" C3 NAG E 2 " pdb=" C5 NAG E 2 " pdb=" O4 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.14 -0.39 2.00e-01 2.50e+01 3.77e+00 ... (remaining 253 not shown) Planarity restraints: 265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.044 2.00e-02 2.50e+03 3.64e-02 1.66e+01 pdb=" C7 NAG E 1 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.044 2.00e-02 2.50e+03 3.63e-02 1.65e+01 pdb=" C7 NAG E 2 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 94 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" C TYR B 94 " 0.038 2.00e-02 2.50e+03 pdb=" O TYR B 94 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS B 95 " -0.013 2.00e-02 2.50e+03 ... (remaining 262 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 536 2.86 - 3.37: 1257 3.37 - 3.88: 2074 3.88 - 4.39: 2123 4.39 - 4.90: 3730 Nonbonded interactions: 9720 Sorted by model distance: nonbonded pdb=" OH TYR A 535 " pdb=" OE1 GLU A 537 " model vdw 2.349 3.040 nonbonded pdb=" O GLN A 504 " pdb=" N SER A 525 " model vdw 2.400 3.120 nonbonded pdb=" OD1 ASN A 548 " pdb=" O5 NAG D 1 " model vdw 2.427 3.040 nonbonded pdb=" O3 NAG C 1 " pdb=" O5 NAG C 2 " model vdw 2.429 3.040 nonbonded pdb=" O ASN A 548 " pdb=" OD1 ASN A 548 " model vdw 2.430 3.040 ... (remaining 9715 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.770 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3767 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 : 0.009 0.042 1458 Z= 0.603 Angle : 1.535 11.650 1991 Z= 0.995 Chirality : 0.079 0.461 256 Planarity : 0.006 0.036 262 Dihedral : 22.405 104.975 527 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 27.16 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.55), residues: 211 helix: None (None), residues: 0 sheet: -0.20 (0.64), residues: 65 loop : -1.45 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.001 0.000 HIS A 578 PHE 0.003 0.001 PHE A 536 TYR 0.003 0.001 TYR A 564 ARG 0.001 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.145 Fit side-chains REVERT: A 560 ASP cc_start: 0.6964 (t0) cc_final: 0.6485 (t0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1326 time to fit residues: 3.5845 Evaluate side-chains 20 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 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: 0.4034 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 1458 Z= 0.291 Angle : 0.778 5.759 1991 Z= 0.412 Chirality : 0.056 0.232 256 Planarity : 0.004 0.017 262 Dihedral : 19.683 84.708 365 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.70 % Allowed : 24.69 % Favored : 71.60 % 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: -2.13 (0.51), residues: 211 helix: None (None), residues: 0 sheet: -0.91 (0.56), residues: 68 loop : -1.76 (0.47), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.003 0.001 HIS A 506 PHE 0.032 0.003 PHE A 566 TYR 0.024 0.004 TYR A 557 ARG 0.001 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.151 Fit side-chains REVERT: A 527 GLU cc_start: 0.6437 (pp20) cc_final: 0.6218 (pp20) REVERT: A 560 ASP cc_start: 0.7054 (t0) cc_final: 0.6558 (t0) outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 0.1149 time to fit residues: 3.0478 Evaluate side-chains 20 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.4336 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 1458 Z= 0.463 Angle : 1.017 9.274 1991 Z= 0.519 Chirality : 0.067 0.264 256 Planarity : 0.005 0.024 262 Dihedral : 19.049 78.997 365 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 4.94 % Allowed : 29.63 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 20.00 % 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: -2.49 (0.53), residues: 211 helix: None (None), residues: 0 sheet: -1.39 (0.60), residues: 65 loop : -1.88 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.003 0.001 HIS A 578 PHE 0.054 0.004 PHE A 566 TYR 0.031 0.005 TYR A 511 ARG 0.002 0.001 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.148 Fit side-chains REVERT: A 527 GLU cc_start: 0.6748 (pp20) cc_final: 0.6503 (pp20) REVERT: A 560 ASP cc_start: 0.7079 (t0) cc_final: 0.6575 (t0) outliers start: 4 outliers final: 3 residues processed: 21 average time/residue: 0.1154 time to fit residues: 2.9201 Evaluate side-chains 21 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 505 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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: 0.4226 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1458 Z= 0.200 Angle : 0.716 8.014 1991 Z= 0.359 Chirality : 0.054 0.256 256 Planarity : 0.003 0.014 262 Dihedral : 15.132 62.674 365 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.70 % Allowed : 28.40 % Favored : 67.90 % 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: -2.31 (0.54), residues: 211 helix: None (None), residues: 0 sheet: -1.39 (0.62), residues: 61 loop : -1.68 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.001 0.000 HIS A 494 PHE 0.015 0.002 PHE A 566 TYR 0.010 0.001 TYR A 557 ARG 0.002 0.001 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.192 Fit side-chains REVERT: A 527 GLU cc_start: 0.6674 (pp20) cc_final: 0.6388 (pp20) REVERT: A 560 ASP cc_start: 0.6982 (t0) cc_final: 0.6438 (t0) outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.1159 time to fit residues: 3.2119 Evaluate side-chains 21 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4421 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 1458 Z= 0.391 Angle : 0.904 8.251 1991 Z= 0.459 Chirality : 0.061 0.283 256 Planarity : 0.004 0.018 262 Dihedral : 14.249 67.964 365 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer: Outliers : 6.17 % Allowed : 28.40 % Favored : 65.43 % 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: -2.43 (0.55), residues: 211 helix: None (None), residues: 0 sheet: -1.29 (0.64), residues: 65 loop : -1.87 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.003 0.002 HIS A 578 PHE 0.039 0.004 PHE A 566 TYR 0.030 0.004 TYR A 511 ARG 0.002 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 0.153 Fit side-chains REVERT: A 527 GLU cc_start: 0.6785 (pp20) cc_final: 0.6446 (pp20) REVERT: A 560 ASP cc_start: 0.7011 (t0) cc_final: 0.6480 (t0) outliers start: 5 outliers final: 5 residues processed: 21 average time/residue: 0.0952 time to fit residues: 2.5048 Evaluate side-chains 23 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 567 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.4329 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1458 Z= 0.209 Angle : 0.712 8.154 1991 Z= 0.357 Chirality : 0.053 0.290 256 Planarity : 0.003 0.017 262 Dihedral : 12.002 59.074 365 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.70 % Allowed : 29.63 % Favored : 66.67 % 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: -2.24 (0.54), residues: 211 helix: None (None), residues: 0 sheet: -1.17 (0.64), residues: 59 loop : -1.72 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.002 0.001 HIS A 494 PHE 0.019 0.002 PHE A 566 TYR 0.008 0.001 TYR A 511 ARG 0.002 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.139 Fit side-chains REVERT: A 491 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6320 (mtm-85) REVERT: A 527 GLU cc_start: 0.6730 (pp20) cc_final: 0.6420 (pp20) REVERT: A 560 ASP cc_start: 0.6967 (t0) cc_final: 0.6388 (t0) outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 0.1162 time to fit residues: 3.0824 Evaluate side-chains 22 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.4458 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 1458 Z= 0.325 Angle : 0.840 5.776 1991 Z= 0.427 Chirality : 0.058 0.329 256 Planarity : 0.004 0.018 262 Dihedral : 11.086 48.218 365 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.74 % Favored : 86.26 % Rotamer: Outliers : 4.94 % Allowed : 28.40 % Favored : 66.67 % 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: -2.43 (0.54), residues: 211 helix: -3.99 (1.51), residues: 6 sheet: -1.32 (0.64), residues: 59 loop : -1.72 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.003 0.001 HIS A 578 PHE 0.033 0.004 PHE A 566 TYR 0.022 0.002 TYR A 511 ARG 0.001 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.150 Fit side-chains REVERT: A 491 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6343 (mtm-85) REVERT: A 527 GLU cc_start: 0.6839 (pp20) cc_final: 0.6499 (pp20) REVERT: A 560 ASP cc_start: 0.6998 (t0) cc_final: 0.6456 (t0) outliers start: 4 outliers final: 3 residues processed: 20 average time/residue: 0.0951 time to fit residues: 2.3846 Evaluate side-chains 22 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 567 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.4474 moved from start: 0.6777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 1458 Z= 0.324 Angle : 0.802 6.037 1991 Z= 0.404 Chirality : 0.055 0.283 256 Planarity : 0.003 0.022 262 Dihedral : 10.162 41.648 365 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 4.94 % Allowed : 28.40 % Favored : 66.67 % 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: -2.33 (0.55), residues: 211 helix: None (None), residues: 0 sheet: -1.27 (0.64), residues: 59 loop : -1.77 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.004 0.001 HIS A 494 PHE 0.030 0.003 PHE A 566 TYR 0.020 0.002 TYR A 511 ARG 0.001 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.156 Fit side-chains REVERT: A 491 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6294 (mtm-85) REVERT: A 527 GLU cc_start: 0.6813 (pp20) cc_final: 0.6507 (pp20) REVERT: A 560 ASP cc_start: 0.7033 (t0) cc_final: 0.6486 (t0) outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 0.0907 time to fit residues: 2.5104 Evaluate side-chains 22 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 567 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 0.2980 chunk 14 optimal weight: 0.0670 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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: 0.4413 moved from start: 0.6796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1458 Z= 0.216 Angle : 0.721 5.889 1991 Z= 0.361 Chirality : 0.051 0.299 256 Planarity : 0.003 0.023 262 Dihedral : 9.026 36.539 365 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 4.94 % Allowed : 30.86 % Favored : 64.20 % 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: -2.19 (0.55), residues: 211 helix: None (None), residues: 0 sheet: -0.98 (0.66), residues: 59 loop : -1.76 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.003 0.001 HIS A 494 PHE 0.015 0.002 PHE A 566 TYR 0.009 0.001 TYR A 511 ARG 0.002 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.153 Fit side-chains REVERT: A 491 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6186 (mtm-85) REVERT: A 527 GLU cc_start: 0.6775 (pp20) cc_final: 0.6474 (pp20) REVERT: A 560 ASP cc_start: 0.6937 (t0) cc_final: 0.6354 (t0) outliers start: 4 outliers final: 3 residues processed: 21 average time/residue: 0.0941 time to fit residues: 2.4714 Evaluate side-chains 22 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 567 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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: 0.4561 moved from start: 0.7294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 1458 Z= 0.487 Angle : 0.948 6.548 1991 Z= 0.483 Chirality : 0.059 0.325 256 Planarity : 0.004 0.026 262 Dihedral : 11.376 39.896 365 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.22 % Favored : 85.78 % Rotamer: Outliers : 4.94 % Allowed : 30.86 % Favored : 64.20 % 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: -2.23 (0.55), residues: 211 helix: None (None), residues: 0 sheet: -1.11 (0.66), residues: 56 loop : -1.74 (0.48), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.006 0.002 HIS A 494 PHE 0.044 0.005 PHE A 566 TYR 0.028 0.004 TYR A 511 ARG 0.003 0.001 ARG A 570 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 422 Ramachandran restraints generated. 211 Oldfield, 0 Emsley, 211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.149 Fit side-chains REVERT: A 491 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6285 (mtm-85) REVERT: A 527 GLU cc_start: 0.6897 (pp20) cc_final: 0.6575 (pp20) REVERT: A 560 ASP cc_start: 0.7052 (t0) cc_final: 0.6571 (t0) outliers start: 4 outliers final: 2 residues processed: 21 average time/residue: 0.0926 time to fit residues: 2.4403 Evaluate side-chains 21 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 567 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.0060 chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.170244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.156082 restraints weight = 3243.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.158622 restraints weight = 2267.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.160326 restraints weight = 1692.360| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 moved from start: 0.7201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1458 Z= 0.225 Angle : 0.729 4.919 1991 Z= 0.373 Chirality : 0.051 0.299 256 Planarity : 0.003 0.028 262 Dihedral : 9.244 33.269 365 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 3.70 % Allowed : 30.86 % Favored : 65.43 % 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: -2.14 (0.55), residues: 211 helix: None (None), residues: 0 sheet: -0.85 (0.67), residues: 56 loop : -1.76 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.004 0.001 HIS A 494 PHE 0.018 0.002 PHE A 566 TYR 0.011 0.002 TYR A 511 ARG 0.002 0.000 ARG A 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 936.97 seconds wall clock time: 17 minutes 7.51 seconds (1027.51 seconds total)