Starting phenix.real_space_refine on Thu Jul 18 16:56:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoa_42432/07_2024/8uoa_42432_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoa_42432/07_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_42432/07_2024/8uoa_42432.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoa_42432/07_2024/8uoa_42432.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoa_42432/07_2024/8uoa_42432_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uoa_42432/07_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-5388/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: 2.57, per 1000 atoms: 1.78 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: 0.70 Conformation dependent library (CDL) restraints added in 308.9 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: 0.23 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: 0.34 Time building geometry restraints manager: 0.74 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 2.440 nonbonded pdb=" O GLN A 504 " pdb=" N SER A 525 " model vdw 2.400 2.520 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 2.440 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 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: 3.500 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.140 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.600 ------------------------------------------------------------------------------- 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 : 0.151 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: 0.1232 time to fit residues: 3.3417 Evaluate side-chains 20 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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: 0.7980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.3905 moved from start: 0.1913 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= 0.205 Angle : 0.690 6.765 1991 Z= 0.359 Chirality : 0.052 0.230 256 Planarity : 0.003 0.016 262 Dihedral : 19.298 86.059 365 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.47 % Allowed : 25.93 % 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: -1.90 (0.52), residues: 211 helix: None (None), residues: 0 sheet: -0.44 (0.60), residues: 66 loop : -1.77 (0.46), residues: 145 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 0.014 0.002 PHE A 566 TYR 0.020 0.002 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 19 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.148 Fit side-chains REVERT: A 560 ASP cc_start: 0.6994 (t0) cc_final: 0.6507 (t0) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.1203 time to fit residues: 2.6327 Evaluate side-chains 18 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.0570 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4118 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 1458 Z= 0.267 Angle : 0.742 7.100 1991 Z= 0.380 Chirality : 0.058 0.278 256 Planarity : 0.003 0.015 262 Dihedral : 17.313 70.748 365 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 8.64 % Allowed : 20.99 % Favored : 70.37 % 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: -2.01 (0.52), residues: 211 helix: None (None), residues: 0 sheet: -0.90 (0.62), residues: 59 loop : -1.61 (0.46), 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 0.033 0.003 PHE A 566 TYR 0.014 0.002 TYR A 511 ARG 0.002 0.000 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 26 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 19 time to evaluate : 0.144 Fit side-chains REVERT: A 527 GLU cc_start: 0.6494 (pp20) cc_final: 0.6217 (pp20) REVERT: A 560 ASP cc_start: 0.7056 (t0) cc_final: 0.6529 (t0) outliers start: 7 outliers final: 5 residues processed: 24 average time/residue: 0.1029 time to fit residues: 2.9975 Evaluate side-chains 24 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 513 ASN Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 555 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.4298 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 1458 Z= 0.354 Angle : 0.879 8.269 1991 Z= 0.438 Chirality : 0.062 0.268 256 Planarity : 0.004 0.019 262 Dihedral : 15.586 67.304 365 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 7.41 % Allowed : 23.46 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.55), residues: 211 helix: None (None), residues: 0 sheet: -0.94 (0.62), residues: 65 loop : -1.70 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.002 0.001 HIS A 578 PHE 0.043 0.004 PHE A 566 TYR 0.028 0.004 TYR A 511 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 26 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.145 Fit side-chains REVERT: A 527 GLU cc_start: 0.6703 (pp20) cc_final: 0.6369 (pp20) REVERT: A 560 ASP cc_start: 0.6990 (t0) cc_final: 0.6480 (t0) outliers start: 6 outliers final: 5 residues processed: 24 average time/residue: 0.1074 time to fit residues: 3.1053 Evaluate side-chains 24 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 513 ASN Chi-restraints excluded: chain A residue 543 ASN 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: 2.9990 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.4278 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1458 Z= 0.253 Angle : 0.733 8.728 1991 Z= 0.365 Chirality : 0.055 0.279 256 Planarity : 0.003 0.016 262 Dihedral : 13.174 58.800 365 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 8.64 % Allowed : 25.93 % 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: -2.00 (0.54), residues: 211 helix: None (None), residues: 0 sheet: -0.84 (0.65), residues: 59 loop : -1.63 (0.48), residues: 152 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 0.022 0.002 PHE A 566 TYR 0.016 0.002 TYR A 511 ARG 0.002 0.000 ARG A 547 *********************** 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 25 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 18 time to evaluate : 0.156 Fit side-chains REVERT: A 527 GLU cc_start: 0.6706 (pp20) cc_final: 0.6390 (pp20) REVERT: A 560 ASP cc_start: 0.6952 (t0) cc_final: 0.6393 (t0) outliers start: 7 outliers final: 6 residues processed: 23 average time/residue: 0.1145 time to fit residues: 3.1694 Evaluate side-chains 24 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 18 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 503 ASN Chi-restraints excluded: chain A residue 513 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: 2.9990 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.4476 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 1458 Z= 0.443 Angle : 0.946 8.188 1991 Z= 0.481 Chirality : 0.061 0.269 256 Planarity : 0.004 0.020 262 Dihedral : 13.073 58.363 365 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer: Outliers : 8.64 % Allowed : 32.10 % Favored : 59.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.53), residues: 211 helix: None (None), residues: 0 sheet: -1.30 (0.65), residues: 59 loop : -1.98 (0.46), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.004 0.002 HIS A 578 PHE 0.041 0.004 PHE A 566 TYR 0.031 0.004 TYR A 511 ARG 0.001 0.000 ARG A 570 *********************** 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 25 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 18 time to evaluate : 0.144 Fit side-chains REVERT: A 491 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6332 (mtm-85) REVERT: A 527 GLU cc_start: 0.6831 (pp20) cc_final: 0.6482 (pp20) REVERT: A 560 ASP cc_start: 0.7047 (t0) cc_final: 0.6541 (t0) outliers start: 7 outliers final: 6 residues processed: 22 average time/residue: 0.1126 time to fit residues: 2.9769 Evaluate side-chains 25 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 18 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 513 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 567 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.4429 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 1458 Z= 0.306 Angle : 0.797 7.334 1991 Z= 0.400 Chirality : 0.057 0.290 256 Planarity : 0.003 0.019 262 Dihedral : 11.379 50.004 365 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 8.64 % Allowed : 30.86 % Favored : 60.49 % 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: -2.45 (0.54), residues: 211 helix: None (None), residues: 0 sheet: -1.26 (0.65), residues: 59 loop : -1.90 (0.47), 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 0.031 0.003 PHE A 566 TYR 0.013 0.002 TYR A 511 ARG 0.001 0.000 ARG A 547 *********************** 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 25 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 18 time to evaluate : 0.141 Fit side-chains REVERT: A 491 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6323 (mtm-85) REVERT: A 527 GLU cc_start: 0.6852 (pp20) cc_final: 0.6532 (pp20) REVERT: A 560 ASP cc_start: 0.7091 (t0) cc_final: 0.6525 (t0) outliers start: 7 outliers final: 6 residues processed: 22 average time/residue: 0.1103 time to fit residues: 2.9232 Evaluate side-chains 25 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 18 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 513 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 552 ILE 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: 6.9990 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.4430 moved from start: 0.6418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1458 Z= 0.259 Angle : 0.749 6.593 1991 Z= 0.376 Chirality : 0.055 0.290 256 Planarity : 0.003 0.020 262 Dihedral : 10.550 44.625 365 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % Rotamer: Outliers : 7.41 % Allowed : 32.10 % Favored : 60.49 % 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: -2.46 (0.54), residues: 211 helix: None (None), residues: 0 sheet: -1.18 (0.66), residues: 59 loop : -1.95 (0.46), 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 0.026 0.002 PHE A 566 TYR 0.014 0.002 TYR A 511 ARG 0.001 0.000 ARG A 547 *********************** 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 24 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 18 time to evaluate : 0.154 Fit side-chains REVERT: A 491 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6325 (mtm-85) REVERT: A 527 GLU cc_start: 0.6810 (pp20) cc_final: 0.6484 (pp20) REVERT: A 560 ASP cc_start: 0.6984 (t0) cc_final: 0.6410 (t0) outliers start: 6 outliers final: 5 residues processed: 22 average time/residue: 0.1124 time to fit residues: 3.0108 Evaluate side-chains 24 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 18 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 513 ASN 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: 6.9990 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.4455 moved from start: 0.6797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 1458 Z= 0.292 Angle : 0.768 5.322 1991 Z= 0.392 Chirality : 0.056 0.327 256 Planarity : 0.003 0.021 262 Dihedral : 10.075 43.566 365 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 8.64 % Allowed : 29.63 % Favored : 61.73 % 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: None (None), residues: 0 sheet: -1.08 (0.67), residues: 59 loop : -1.96 (0.47), 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 0.032 0.003 PHE A 566 TYR 0.017 0.002 TYR A 511 ARG 0.001 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 23 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 16 time to evaluate : 0.149 Fit side-chains REVERT: A 491 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6290 (mtm-85) REVERT: A 527 GLU cc_start: 0.6766 (pp20) cc_final: 0.6436 (pp20) REVERT: A 560 ASP cc_start: 0.6981 (t0) cc_final: 0.6435 (t0) outliers start: 7 outliers final: 4 residues processed: 21 average time/residue: 0.0956 time to fit residues: 2.5101 Evaluate side-chains 21 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 16 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 503 ASN 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: 2.9990 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 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: 0.4430 moved from start: 0.6871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 1458 Z= 0.219 Angle : 0.690 5.028 1991 Z= 0.357 Chirality : 0.053 0.325 256 Planarity : 0.003 0.021 262 Dihedral : 8.979 36.845 365 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer: Outliers : 7.41 % Allowed : 30.86 % Favored : 61.73 % 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: -2.11 (0.55), residues: 211 helix: None (None), residues: 0 sheet: -0.74 (0.72), residues: 56 loop : -1.79 (0.47), residues: 155 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 0.021 0.002 PHE A 566 TYR 0.012 0.002 TYR A 511 ARG 0.001 0.000 ARG A 547 ********************** 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: 6 poor density : 16 time to evaluate : 0.143 Fit side-chains REVERT: A 491 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6237 (mtm-85) REVERT: A 527 GLU cc_start: 0.6764 (pp20) cc_final: 0.6438 (pp20) REVERT: A 560 ASP cc_start: 0.6949 (t0) cc_final: 0.6356 (t0) outliers start: 6 outliers final: 4 residues processed: 21 average time/residue: 0.0907 time to fit residues: 2.3658 Evaluate side-chains 21 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 16 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.0770 chunk 2 optimal weight: 0.0370 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.169885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.156589 restraints weight = 3285.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.159123 restraints weight = 2252.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.160935 restraints weight = 1645.375| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.7058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1458 Z= 0.251 Angle : 0.710 5.106 1991 Z= 0.369 Chirality : 0.054 0.317 256 Planarity : 0.003 0.022 262 Dihedral : 9.011 41.334 365 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer: Outliers : 6.17 % Allowed : 32.10 % Favored : 61.73 % 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: -2.09 (0.56), residues: 211 helix: None (None), residues: 0 sheet: -0.75 (0.70), residues: 56 loop : -1.75 (0.48), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.004 0.002 HIS A 494 PHE 0.027 0.003 PHE A 566 TYR 0.015 0.002 TYR A 511 ARG 0.001 0.000 ARG A 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 920.61 seconds wall clock time: 18 minutes 19.97 seconds (1099.97 seconds total)