Starting phenix.real_space_refine on Mon Feb 10 19:28:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uoa_42432/02_2025/8uoa_42432_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uoa_42432/02_2025/8uoa_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/cci-nas-00/data/ceres_data/8uoa_42432/02_2025/8uoa_42432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uoa_42432/02_2025/8uoa_42432.map" model { file = "/net/cci-nas-00/data/ceres_data/8uoa_42432/02_2025/8uoa_42432_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uoa_42432/02_2025/8uoa_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. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 2.74, per 1000 atoms: 1.90 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 - 3.00 Amino acid : True - 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: 0.83 Conformation dependent library (CDL) restraints added in 234.9 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: 0.25 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: 0.36 Time building geometry restraints manager: 0.90 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: 0.00 - 2.33: 1795 2.33 - 4.66: 150 4.66 - 6.99: 35 6.99 - 9.32: 9 9.32 - 11.65: 2 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: 2.240 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.290 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.310 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.131 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: 0.1267 time to fit residues: 3.4197 Evaluate side-chains 20 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. 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: 0.9980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.180582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.165119 restraints weight = 3251.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.168168 restraints weight = 2189.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.170358 restraints weight = 1582.997| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 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 to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.144 Fit side-chains REVERT: A 560 ASP cc_start: 0.7222 (t0) cc_final: 0.7004 (t0) outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 0.1104 time to fit residues: 2.9495 Evaluate side-chains 20 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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 17 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.179615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.164684 restraints weight = 3245.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.167718 restraints weight = 2210.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.169857 restraints weight = 1597.515| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1458 Z= 0.284 Angle : 0.756 7.457 1991 Z= 0.384 Chirality : 0.058 0.249 256 Planarity : 0.003 0.016 262 Dihedral : 17.480 72.715 365 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % 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: -2.12 (0.52), residues: 211 helix: None (None), residues: 0 sheet: -1.01 (0.56), residues: 71 loop : -1.70 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.001 0.000 HIS A 506 PHE 0.029 0.003 PHE A 566 TYR 0.012 0.002 TYR A 511 ARG 0.001 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 22 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.142 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 22 average time/residue: 0.1082 time to fit residues: 2.8841 Evaluate side-chains 20 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.177882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.162672 restraints weight = 3332.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.165573 restraints weight = 2270.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.167675 restraints weight = 1656.622| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1458 Z= 0.275 Angle : 0.806 8.176 1991 Z= 0.407 Chirality : 0.056 0.263 256 Planarity : 0.003 0.017 262 Dihedral : 14.453 65.491 365 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 2.47 % Allowed : 32.10 % 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: -2.26 (0.54), residues: 211 helix: None (None), residues: 0 sheet: -1.16 (0.59), residues: 71 loop : -1.76 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.001 0.001 HIS A 494 PHE 0.031 0.003 PHE A 566 TYR 0.017 0.003 TYR A 511 ARG 0.002 0.000 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 21 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.152 Fit side-chains REVERT: A 560 ASP cc_start: 0.7280 (t0) cc_final: 0.6909 (t0) outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 0.1185 time to fit residues: 2.9904 Evaluate side-chains 21 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.173201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.159221 restraints weight = 3288.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.161833 restraints weight = 2261.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.163752 restraints weight = 1656.813| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 1458 Z= 0.353 Angle : 0.873 7.648 1991 Z= 0.445 Chirality : 0.061 0.313 256 Planarity : 0.004 0.017 262 Dihedral : 12.027 56.602 365 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % Rotamer: Outliers : 7.41 % Allowed : 29.63 % Favored : 62.96 % 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: -1.28 (0.64), residues: 59 loop : -1.74 (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 578 PHE 0.033 0.004 PHE A 566 TYR 0.032 0.004 TYR A 511 ARG 0.002 0.001 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 to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.155 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 23 average time/residue: 0.1198 time to fit residues: 3.2982 Evaluate side-chains 24 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 505 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 0.0970 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.174970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.161005 restraints weight = 3259.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.163702 restraints weight = 2209.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.165529 restraints weight = 1611.994| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1458 Z= 0.238 Angle : 0.761 6.981 1991 Z= 0.381 Chirality : 0.053 0.299 256 Planarity : 0.003 0.020 262 Dihedral : 10.400 47.765 365 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 4.94 % Allowed : 32.10 % Favored : 62.96 % 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: -2.32 (0.52), residues: 211 helix: None (None), residues: 0 sheet: -1.18 (0.65), residues: 59 loop : -1.80 (0.45), 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 0.022 0.002 PHE A 566 TYR 0.011 0.002 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 23 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.155 Fit side-chains REVERT: A 560 ASP cc_start: 0.7201 (t0) cc_final: 0.6956 (t0) outliers start: 4 outliers final: 1 residues processed: 23 average time/residue: 0.1129 time to fit residues: 3.1216 Evaluate side-chains 20 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 6 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4160 r_free = 0.4160 target = 0.171194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.157099 restraints weight = 3306.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.159797 restraints weight = 2261.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.161660 restraints weight = 1641.321| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 1458 Z= 0.352 Angle : 0.825 6.322 1991 Z= 0.425 Chirality : 0.057 0.342 256 Planarity : 0.004 0.031 262 Dihedral : 10.044 44.889 365 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % 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: -2.40 (0.54), residues: 211 helix: None (None), residues: 0 sheet: -1.34 (0.64), residues: 59 loop : -1.80 (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 578 PHE 0.035 0.003 PHE A 566 TYR 0.026 0.003 TYR A 511 ARG 0.003 0.001 ARG A 491 *********************** 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 23 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.124 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 21 average time/residue: 0.0581 time to fit residues: 1.7098 Evaluate side-chains 22 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 494 HIS 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 13 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.168522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.159267 restraints weight = 3368.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.160803 restraints weight = 2444.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.161812 restraints weight = 1879.723| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.7360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.070 1458 Z= 0.653 Angle : 1.204 8.039 1991 Z= 0.608 Chirality : 0.071 0.364 256 Planarity : 0.005 0.026 262 Dihedral : 13.366 49.118 365 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 26.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.69 % Favored : 85.31 % 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: -3.02 (0.54), residues: 211 helix: None (None), residues: 0 sheet: -1.79 (0.64), residues: 65 loop : -2.23 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.007 0.003 HIS A 578 PHE 0.053 0.005 PHE A 566 TYR 0.042 0.005 TYR A 511 ARG 0.002 0.000 ARG A 491 *********************** 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 to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.152 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 21 average time/residue: 0.0589 time to fit residues: 1.7459 Evaluate side-chains 24 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 503 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.167445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.153961 restraints weight = 3144.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.156423 restraints weight = 2148.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.158280 restraints weight = 1588.037| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.7308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 1458 Z= 0.373 Angle : 0.949 6.651 1991 Z= 0.480 Chirality : 0.058 0.326 256 Planarity : 0.004 0.028 262 Dihedral : 12.156 43.757 365 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer: Outliers : 6.17 % Allowed : 27.16 % 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: -3.04 (0.53), residues: 211 helix: -3.68 (1.80), residues: 6 sheet: -1.68 (0.64), residues: 65 loop : -2.21 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 36 HIS 0.005 0.002 HIS A 494 PHE 0.034 0.003 PHE A 566 TYR 0.023 0.003 TYR A 511 ARG 0.001 0.001 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 to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.155 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 21 average time/residue: 0.0703 time to fit residues: 2.0425 Evaluate side-chains 21 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 19 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.169776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.155999 restraints weight = 3274.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.158567 restraints weight = 2233.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.160391 restraints weight = 1635.830| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.7267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1458 Z= 0.239 Angle : 0.842 6.088 1991 Z= 0.426 Chirality : 0.053 0.322 256 Planarity : 0.003 0.029 262 Dihedral : 10.458 36.461 365 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 2.47 % Allowed : 29.63 % 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: -2.68 (0.53), residues: 211 helix: None (None), residues: 0 sheet: -1.24 (0.67), residues: 56 loop : -2.15 (0.46), 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 0.019 0.002 PHE A 566 TYR 0.013 0.002 TYR A 511 ARG 0.000 0.000 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 20 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.144 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 19 average time/residue: 0.0653 time to fit residues: 1.7444 Evaluate side-chains 20 residues out of total 188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE 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 8 optimal weight: 0.1980 chunk 12 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.1980 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.170513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.156573 restraints weight = 3410.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.159205 restraints weight = 2332.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.160970 restraints weight = 1702.639| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.7302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1458 Z= 0.222 Angle : 0.763 6.243 1991 Z= 0.396 Chirality : 0.052 0.286 256 Planarity : 0.003 0.026 262 Dihedral : 9.005 28.242 365 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 2.47 % Allowed : 30.86 % 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: -2.54 (0.52), residues: 211 helix: -3.57 (1.93), residues: 6 sheet: -0.65 (0.70), residues: 47 loop : -2.11 (0.45), residues: 158 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 0.020 0.002 PHE A 566 TYR 0.011 0.002 TYR A 511 ARG 0.000 0.000 ARG A 547 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1058.36 seconds wall clock time: 19 minutes 23.45 seconds (1163.45 seconds total)