Starting phenix.real_space_refine on Wed Mar 5 18:34:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tas_25783/03_2025/7tas_25783.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tas_25783/03_2025/7tas_25783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tas_25783/03_2025/7tas_25783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tas_25783/03_2025/7tas_25783.map" model { file = "/net/cci-nas-00/data/ceres_data/7tas_25783/03_2025/7tas_25783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tas_25783/03_2025/7tas_25783.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2014 2.51 5 N 549 2.21 5 O 570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3147 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 904 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 751 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1454 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.87, per 1000 atoms: 1.23 Number of scatterers: 3147 At special positions: 0 Unit cell: (61, 82, 81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 570 8.00 N 549 7.00 C 2014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.15 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.23 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.17 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 A 1 " - " NAG A 2 " BETA1-6 " NAG A 1 " - " FUC A 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN E 343 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 346.2 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 10.6% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.815A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.877A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.559A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.504A pdb=" N TYR E 421 " --> pdb=" O LYS E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.563A pdb=" N HIS H 59 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.550A pdb=" N ALA L 10 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.550A pdb=" N ALA L 10 " --> pdb=" O THR L 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA6, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.531A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.699A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'E' and resid 473 through 474 100 hydrogen bonds defined for protein. 234 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 911 1.33 - 1.47: 920 1.47 - 1.60: 1382 1.60 - 1.73: 0 1.73 - 1.86: 16 Bond restraints: 3229 Sorted by residual: bond pdb=" N CYS E 391 " pdb=" CA CYS E 391 " ideal model delta sigma weight residual 1.454 1.534 -0.080 1.23e-02 6.61e+03 4.27e+01 bond pdb=" C CYS E 336 " pdb=" O CYS E 336 " ideal model delta sigma weight residual 1.237 1.313 -0.076 1.29e-02 6.01e+03 3.47e+01 bond pdb=" CA ILE L 29 " pdb=" CB ILE L 29 " ideal model delta sigma weight residual 1.544 1.493 0.051 1.17e-02 7.31e+03 1.90e+01 bond pdb=" N CYS E 336 " pdb=" CA CYS E 336 " ideal model delta sigma weight residual 1.454 1.401 0.053 1.29e-02 6.01e+03 1.70e+01 bond pdb=" CA SER L 95 " pdb=" C SER L 95 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.26e-02 6.30e+03 1.20e+01 ... (remaining 3224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 3524 1.69 - 3.37: 709 3.37 - 5.06: 116 5.06 - 6.74: 40 6.74 - 8.43: 12 Bond angle restraints: 4401 Sorted by residual: angle pdb=" C GLN L 6 " pdb=" N PRO L 7 " pdb=" CA PRO L 7 " ideal model delta sigma weight residual 119.66 125.93 -6.27 7.30e-01 1.88e+00 7.38e+01 angle pdb=" C THR E 478 " pdb=" N PRO E 479 " pdb=" CA PRO E 479 " ideal model delta sigma weight residual 119.90 128.33 -8.43 1.05e+00 9.07e-01 6.44e+01 angle pdb=" C PHE E 490 " pdb=" N PRO E 491 " pdb=" CA PRO E 491 " ideal model delta sigma weight residual 119.87 127.54 -7.67 1.04e+00 9.25e-01 5.44e+01 angle pdb=" C VAL L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 120.03 127.01 -6.98 9.90e-01 1.02e+00 4.97e+01 angle pdb=" C ARG L 55 " pdb=" N PRO L 56 " pdb=" CA PRO L 56 " ideal model delta sigma weight residual 120.31 127.17 -6.86 9.80e-01 1.04e+00 4.89e+01 ... (remaining 4396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 1772 15.95 - 31.90: 102 31.90 - 47.84: 20 47.84 - 63.79: 7 63.79 - 79.74: 4 Dihedral angle restraints: 1905 sinusoidal: 720 harmonic: 1185 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 49.70 43.30 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CA SER H 109 " pdb=" C SER H 109 " pdb=" N ASP H 110 " pdb=" CA ASP H 110 " ideal model delta harmonic sigma weight residual -180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" N LYS L 97 " pdb=" C LYS L 97 " pdb=" CA LYS L 97 " pdb=" CB LYS L 97 " ideal model delta harmonic sigma weight residual 122.80 132.21 -9.41 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 1902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 354 0.092 - 0.183: 111 0.183 - 0.275: 14 0.275 - 0.367: 2 0.367 - 0.458: 2 Chirality restraints: 483 Sorted by residual: chirality pdb=" C1 FUC A 3 " pdb=" O6 NAG A 1 " pdb=" C2 FUC A 3 " pdb=" O5 FUC A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" CA CYS E 336 " pdb=" N CYS E 336 " pdb=" C CYS E 336 " pdb=" CB CYS E 336 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA CYS E 391 " pdb=" N CYS E 391 " pdb=" C CYS E 391 " pdb=" CB CYS E 391 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.43e+00 ... (remaining 480 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " 0.207 2.00e-02 2.50e+03 1.75e-01 3.82e+02 pdb=" C7 NAG A 2 " -0.045 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " -0.042 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " -0.283 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.141 2.00e-02 2.50e+03 1.16e-01 1.69e+02 pdb=" C7 NAG A 1 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.105 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.187 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS H 22 " -0.024 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C CYS H 22 " 0.086 2.00e-02 2.50e+03 pdb=" O CYS H 22 " -0.034 2.00e-02 2.50e+03 pdb=" N ALA H 23 " -0.028 2.00e-02 2.50e+03 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 1424 2.94 - 3.43: 2587 3.43 - 3.92: 5073 3.92 - 4.41: 5879 4.41 - 4.90: 9789 Nonbonded interactions: 24752 Sorted by model distance: nonbonded pdb=" O ASP L 93 " pdb=" O LEU L 96 " model vdw 2.452 3.040 nonbonded pdb=" O SER L 68 " pdb=" OG SER L 68 " model vdw 2.453 3.040 nonbonded pdb=" O ILE L 29 " pdb=" C GLY L 30 " model vdw 2.540 3.270 nonbonded pdb=" C ASP E 364 " pdb=" OD1 ASP E 364 " model vdw 2.569 3.270 nonbonded pdb=" OD1 ASP E 364 " pdb=" N SER E 366 " model vdw 2.580 3.120 ... (remaining 24747 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.640 Find NCS groups from input model: 0.030 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.080 3229 Z= 0.858 Angle : 1.497 8.429 4401 Z= 1.025 Chirality : 0.089 0.458 483 Planarity : 0.011 0.175 568 Dihedral : 11.333 79.738 1139 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.69 % Allowed : 3.04 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.38), residues: 409 helix: -5.04 (0.23), residues: 32 sheet: 0.13 (0.41), residues: 139 loop : -0.45 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP H 47 HIS 0.006 0.002 HIS H 32 PHE 0.020 0.003 PHE E 497 TYR 0.033 0.005 TYR H 95 ARG 0.002 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.339 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 70 average time/residue: 0.2381 time to fit residues: 19.0634 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 392 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 HIS H 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099865 restraints weight = 4799.704| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.83 r_work: 0.3107 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3229 Z= 0.231 Angle : 0.642 9.126 4401 Z= 0.334 Chirality : 0.046 0.142 483 Planarity : 0.004 0.033 568 Dihedral : 4.916 30.254 518 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.71 % Favored : 98.04 % Rotamer: Outliers : 2.03 % Allowed : 9.46 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.40), residues: 409 helix: -4.26 (0.66), residues: 26 sheet: 0.32 (0.40), residues: 139 loop : 0.08 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 353 HIS 0.007 0.002 HIS H 35 PHE 0.012 0.001 PHE E 377 TYR 0.013 0.002 TYR H 60 ARG 0.006 0.001 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.365 Fit side-chains REVERT: H 19 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7636 (ttp80) outliers start: 6 outliers final: 4 residues processed: 61 average time/residue: 0.2303 time to fit residues: 16.1413 Evaluate side-chains 51 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 461 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.0270 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.0000 chunk 26 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 overall best weight: 0.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.107672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099902 restraints weight = 4791.913| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.89 r_work: 0.3099 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3229 Z= 0.145 Angle : 0.556 8.733 4401 Z= 0.282 Chirality : 0.043 0.142 483 Planarity : 0.003 0.030 568 Dihedral : 4.392 28.636 516 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.35 % Allowed : 11.15 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.41), residues: 409 helix: -3.85 (0.61), residues: 32 sheet: 0.52 (0.41), residues: 139 loop : 0.38 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.014 0.001 PHE E 490 TYR 0.010 0.001 TYR E 453 ARG 0.003 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.355 Fit side-chains REVERT: H 34 MET cc_start: 0.8969 (mmm) cc_final: 0.8744 (mmm) REVERT: H 102 ARG cc_start: 0.8818 (mtm110) cc_final: 0.8357 (mtm110) REVERT: L 48 LEU cc_start: 0.9167 (mt) cc_final: 0.8961 (mt) outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 0.2369 time to fit residues: 15.7276 Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 19 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 23 optimal weight: 0.0070 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 16 GLN E 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.106236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.098353 restraints weight = 4858.386| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.94 r_work: 0.3076 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3229 Z= 0.175 Angle : 0.547 8.657 4401 Z= 0.273 Chirality : 0.043 0.134 483 Planarity : 0.003 0.031 568 Dihedral : 4.115 20.250 514 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.04 % Allowed : 10.14 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.42), residues: 409 helix: -3.43 (0.78), residues: 32 sheet: 0.80 (0.43), residues: 138 loop : 0.39 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.006 0.001 PHE E 377 TYR 0.010 0.001 TYR H 60 ARG 0.003 0.000 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.547 Fit side-chains REVERT: E 490 PHE cc_start: 0.8508 (t80) cc_final: 0.8228 (t80) outliers start: 9 outliers final: 7 residues processed: 56 average time/residue: 0.2626 time to fit residues: 16.8424 Evaluate side-chains 57 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.0010 chunk 22 optimal weight: 0.2980 chunk 29 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 16 GLN L 39 HIS ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.098140 restraints weight = 4754.343| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.91 r_work: 0.3072 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3229 Z= 0.180 Angle : 0.546 8.635 4401 Z= 0.269 Chirality : 0.043 0.137 483 Planarity : 0.003 0.032 568 Dihedral : 4.091 19.686 514 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.36 % Allowed : 11.49 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.42), residues: 409 helix: -3.50 (0.70), residues: 32 sheet: 0.96 (0.43), residues: 138 loop : 0.37 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE L 100 TYR 0.009 0.001 TYR H 95 ARG 0.005 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.310 Fit side-chains REVERT: H 34 MET cc_start: 0.9014 (mmm) cc_final: 0.8673 (mmm) REVERT: H 102 ARG cc_start: 0.8806 (mtm110) cc_final: 0.8255 (mtm110) REVERT: E 466 ARG cc_start: 0.8607 (ttp-110) cc_final: 0.8268 (ttp-110) outliers start: 7 outliers final: 5 residues processed: 57 average time/residue: 0.2383 time to fit residues: 15.5868 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 0.7980 chunk 10 optimal weight: 0.0060 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.106056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098426 restraints weight = 4872.870| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.86 r_work: 0.3077 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3229 Z= 0.162 Angle : 0.564 8.594 4401 Z= 0.279 Chirality : 0.044 0.207 483 Planarity : 0.003 0.032 568 Dihedral : 4.092 19.679 514 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.03 % Allowed : 12.50 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.42), residues: 409 helix: -3.55 (0.67), residues: 32 sheet: 1.04 (0.44), residues: 138 loop : 0.34 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE L 100 TYR 0.009 0.001 TYR H 60 ARG 0.005 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.323 Fit side-chains REVERT: E 490 PHE cc_start: 0.8468 (t80) cc_final: 0.8174 (t80) outliers start: 6 outliers final: 6 residues processed: 54 average time/residue: 0.2466 time to fit residues: 15.3492 Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.095403 restraints weight = 4828.148| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.80 r_work: 0.3037 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3229 Z= 0.269 Angle : 0.595 8.593 4401 Z= 0.297 Chirality : 0.045 0.141 483 Planarity : 0.004 0.033 568 Dihedral : 4.235 19.683 514 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.70 % Allowed : 12.84 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.42), residues: 409 helix: -3.60 (0.65), residues: 32 sheet: 0.95 (0.44), residues: 138 loop : 0.22 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE E 429 TYR 0.013 0.002 TYR H 60 ARG 0.006 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.328 Fit side-chains REVERT: E 466 ARG cc_start: 0.8596 (ttp-110) cc_final: 0.8295 (ttp-110) REVERT: E 490 PHE cc_start: 0.8467 (t80) cc_final: 0.8202 (t80) outliers start: 8 outliers final: 6 residues processed: 58 average time/residue: 0.2468 time to fit residues: 16.3988 Evaluate side-chains 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 0.0470 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.0050 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 overall best weight: 0.4292 ------------------------------------------------------------------------------- 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 = 0.3243 r_free = 0.3243 target = 0.104750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.097261 restraints weight = 4817.585| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.83 r_work: 0.3065 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3229 Z= 0.160 Angle : 0.553 8.661 4401 Z= 0.269 Chirality : 0.042 0.145 483 Planarity : 0.003 0.033 568 Dihedral : 4.128 19.947 514 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.69 % Allowed : 13.51 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.42), residues: 409 helix: -3.64 (0.62), residues: 32 sheet: 0.93 (0.44), residues: 138 loop : 0.25 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.006 0.001 PHE E 377 TYR 0.009 0.001 TYR E 453 ARG 0.006 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.349 Fit side-chains REVERT: E 490 PHE cc_start: 0.8498 (t80) cc_final: 0.8246 (t80) outliers start: 5 outliers final: 5 residues processed: 53 average time/residue: 0.2390 time to fit residues: 14.6774 Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 chunk 23 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 12 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.0270 chunk 39 optimal weight: 0.5980 overall best weight: 0.1014 ------------------------------------------------------------------------------- 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 = 0.3290 r_free = 0.3290 target = 0.108137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.100268 restraints weight = 4801.665| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.95 r_work: 0.3108 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3229 Z= 0.108 Angle : 0.526 8.627 4401 Z= 0.251 Chirality : 0.041 0.137 483 Planarity : 0.003 0.032 568 Dihedral : 3.953 19.534 514 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.01 % Allowed : 14.53 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.42), residues: 409 helix: -3.52 (0.64), residues: 32 sheet: 1.04 (0.43), residues: 138 loop : 0.39 (0.42), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 HIS 0.002 0.000 HIS H 35 PHE 0.007 0.001 PHE L 100 TYR 0.007 0.001 TYR L 37 ARG 0.007 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.348 Fit side-chains REVERT: H 34 MET cc_start: 0.8928 (mmm) cc_final: 0.8560 (mmm) REVERT: H 102 ARG cc_start: 0.8743 (mtm110) cc_final: 0.8447 (mtm110) REVERT: E 423 TYR cc_start: 0.8958 (t80) cc_final: 0.8661 (t80) REVERT: E 490 PHE cc_start: 0.8470 (t80) cc_final: 0.8142 (t80) outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 0.2336 time to fit residues: 15.3667 Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 0.0000 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.103871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.096171 restraints weight = 4744.733| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.90 r_work: 0.3049 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3229 Z= 0.245 Angle : 0.576 8.312 4401 Z= 0.278 Chirality : 0.043 0.137 483 Planarity : 0.004 0.036 568 Dihedral : 4.016 19.429 514 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.35 % Allowed : 14.86 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.41), residues: 409 helix: -3.53 (0.65), residues: 32 sheet: 1.01 (0.43), residues: 138 loop : 0.25 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE L 100 TYR 0.011 0.001 TYR E 351 ARG 0.006 0.001 ARG H 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.322 Fit side-chains REVERT: L 47 LEU cc_start: 0.9138 (tp) cc_final: 0.8920 (tp) REVERT: E 466 ARG cc_start: 0.8633 (ttp-110) cc_final: 0.8321 (ttp-110) REVERT: E 490 PHE cc_start: 0.8517 (t80) cc_final: 0.8236 (t80) outliers start: 4 outliers final: 4 residues processed: 57 average time/residue: 0.2416 time to fit residues: 15.7245 Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.102710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.095209 restraints weight = 4909.535| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.83 r_work: 0.3039 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3229 Z= 0.277 Angle : 0.613 8.319 4401 Z= 0.300 Chirality : 0.045 0.145 483 Planarity : 0.004 0.036 568 Dihedral : 4.175 19.901 514 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.36 % Allowed : 14.19 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.41), residues: 409 helix: -3.56 (0.65), residues: 32 sheet: 0.88 (0.43), residues: 138 loop : 0.11 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE E 429 TYR 0.012 0.001 TYR E 351 ARG 0.006 0.001 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2298.36 seconds wall clock time: 40 minutes 22.13 seconds (2422.13 seconds total)