Starting phenix.real_space_refine on Thu Nov 14 04:19:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j75_36027/11_2024/8j75_36027.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j75_36027/11_2024/8j75_36027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j75_36027/11_2024/8j75_36027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j75_36027/11_2024/8j75_36027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j75_36027/11_2024/8j75_36027.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j75_36027/11_2024/8j75_36027.cif" } resolution = 3.6 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= 0.004 sd= 0.074 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 19 5.16 5 C 2625 2.51 5 N 605 2.21 5 O 707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3956 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3887 Classifications: {'peptide': 515} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 22, 'TRANS': 492} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" 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: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'HC6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.38, per 1000 atoms: 0.85 Number of scatterers: 3956 At special positions: 0 Unit cell: (87.74, 73.8, 86.1, 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 19 16.00 O 707 8.00 N 605 7.00 C 2625 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 B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 301 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 706.6 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 1 sheets defined 76.7% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 4 through 30 removed outlier: 3.934A pdb=" N LEU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.559A pdb=" N GLY A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 81 through 84 Processing helix chain 'A' and resid 85 through 102 removed outlier: 4.702A pdb=" N ILE A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.712A pdb=" N LYS A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY A 110 " --> pdb=" O MET A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 123 through 157 removed outlier: 3.555A pdb=" N LEU A 129 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 160 through 179 removed outlier: 4.023A pdb=" N SER A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 208 removed outlier: 3.675A pdb=" N VAL A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 266 through 297 removed outlier: 4.023A pdb=" N ILE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 309 through 313 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.620A pdb=" N ILE A 322 " --> pdb=" O MET A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 368 removed outlier: 3.973A pdb=" N PHE A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 366 " --> pdb=" O ASN A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 398 removed outlier: 3.538A pdb=" N VAL A 378 " --> pdb=" O ASP A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 427 removed outlier: 4.641A pdb=" N PHE A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 431 through 450 removed outlier: 3.596A pdb=" N ALA A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 467 273 hydrogen bonds defined for protein. 804 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: 1.08 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1132 1.34 - 1.46: 833 1.46 - 1.58: 2066 1.58 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 4065 Sorted by residual: bond pdb=" C TYR A 462 " pdb=" N PRO A 463 " ideal model delta sigma weight residual 1.332 1.366 -0.035 1.30e-02 5.92e+03 7.06e+00 bond pdb=" N VAL A 237 " pdb=" CA VAL A 237 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.12e+00 bond pdb=" CA TYR A 462 " pdb=" CB TYR A 462 " ideal model delta sigma weight residual 1.528 1.489 0.039 1.57e-02 4.06e+03 6.11e+00 bond pdb=" N TYR A 67 " pdb=" CA TYR A 67 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.31e+00 bond pdb=" N GLU A 236 " pdb=" CA GLU A 236 " ideal model delta sigma weight residual 1.462 1.487 -0.024 1.20e-02 6.94e+03 4.13e+00 ... (remaining 4060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 5368 1.70 - 3.40: 147 3.40 - 5.10: 32 5.10 - 6.81: 11 6.81 - 8.51: 4 Bond angle restraints: 5562 Sorted by residual: angle pdb=" N PRO A 508 " pdb=" CA PRO A 508 " pdb=" C PRO A 508 " ideal model delta sigma weight residual 110.70 114.66 -3.96 1.22e+00 6.72e-01 1.05e+01 angle pdb=" CB MET A 139 " pdb=" CG MET A 139 " pdb=" SD MET A 139 " ideal model delta sigma weight residual 112.70 121.21 -8.51 3.00e+00 1.11e-01 8.04e+00 angle pdb=" N GLY A 79 " pdb=" CA GLY A 79 " pdb=" C GLY A 79 " ideal model delta sigma weight residual 114.67 110.71 3.96 1.41e+00 5.03e-01 7.90e+00 angle pdb=" N TYR A 462 " pdb=" CA TYR A 462 " pdb=" C TYR A 462 " ideal model delta sigma weight residual 109.48 113.24 -3.76 1.44e+00 4.82e-01 6.81e+00 angle pdb=" N VAL A 220 " pdb=" CA VAL A 220 " pdb=" C VAL A 220 " ideal model delta sigma weight residual 109.34 114.63 -5.29 2.08e+00 2.31e-01 6.48e+00 ... (remaining 5557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.99: 2188 25.99 - 51.98: 136 51.98 - 77.97: 17 77.97 - 103.96: 21 103.96 - 129.95: 4 Dihedral angle restraints: 2366 sinusoidal: 887 harmonic: 1479 Sorted by residual: dihedral pdb=" CAS HC6 A 601 " pdb=" CAU HC6 A 601 " pdb=" OAT HC6 A 601 " pdb=" CAV HC6 A 601 " ideal model delta sinusoidal sigma weight residual -59.78 70.17 -129.95 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" CAB HC6 A 601 " pdb=" CAF HC6 A 601 " pdb=" OAE HC6 A 601 " pdb=" CAD HC6 A 601 " ideal model delta sinusoidal sigma weight residual 59.04 -70.03 129.07 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.99 108.72 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 2363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 523 0.055 - 0.109: 119 0.109 - 0.164: 7 0.164 - 0.219: 1 0.219 - 0.274: 2 Chirality restraints: 652 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA VAL A 237 " pdb=" N VAL A 237 " pdb=" C VAL A 237 " pdb=" CB VAL A 237 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA TYR A 238 " pdb=" N TYR A 238 " pdb=" C TYR A 238 " pdb=" CB TYR A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.60e-01 ... (remaining 649 not shown) Planarity restraints: 675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAD HC6 A 601 " -0.030 2.00e-02 2.50e+03 1.76e-02 6.18e+00 pdb=" CAG HC6 A 601 " 0.009 2.00e-02 2.50e+03 pdb=" CAH HC6 A 601 " 0.010 2.00e-02 2.50e+03 pdb=" CAI HC6 A 601 " 0.010 2.00e-02 2.50e+03 pdb=" CAJ HC6 A 601 " 0.009 2.00e-02 2.50e+03 pdb=" CAK HC6 A 601 " 0.010 2.00e-02 2.50e+03 pdb=" CAL HC6 A 601 " 0.011 2.00e-02 2.50e+03 pdb=" CAM HC6 A 601 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 451 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A 452 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 461 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C PHE A 461 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE A 461 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 462 " -0.010 2.00e-02 2.50e+03 ... (remaining 672 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1037 2.79 - 3.32: 3999 3.32 - 3.84: 6572 3.84 - 4.37: 7148 4.37 - 4.90: 12449 Nonbonded interactions: 31205 Sorted by model distance: nonbonded pdb=" O3 NAG B 2 " pdb=" O2 BMA B 3 " model vdw 2.261 3.040 nonbonded pdb=" O ALA A 390 " pdb=" OG1 THR A 393 " model vdw 2.263 3.040 nonbonded pdb=" O ALA A 213 " pdb=" OG SER A 297 " model vdw 2.312 3.040 nonbonded pdb=" NH2 ARG A 47 " pdb=" O TYR A 111 " model vdw 2.313 3.120 nonbonded pdb=" N SER A 34 " pdb=" OE1 GLU A 37 " model vdw 2.354 3.120 ... (remaining 31200 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 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: 0.730 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 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 : 0.004 0.039 4065 Z= 0.248 Angle : 0.721 8.507 5562 Z= 0.371 Chirality : 0.045 0.274 652 Planarity : 0.005 0.046 674 Dihedral : 20.252 129.948 1430 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.99 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 26.97 % Favored : 73.03 % 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: 0.40 (0.40), residues: 513 helix: 1.45 (0.29), residues: 352 sheet: None (None), residues: 0 loop : -2.53 (0.50), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 228 HIS 0.001 0.000 HIS A 4 PHE 0.014 0.001 PHE A 244 TYR 0.017 0.001 TYR A 175 ARG 0.007 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.364 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1538 time to fit residues: 16.7887 Evaluate side-chains 84 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4065 Z= 0.204 Angle : 0.680 7.951 5562 Z= 0.332 Chirality : 0.044 0.293 652 Planarity : 0.004 0.033 674 Dihedral : 14.843 89.963 650 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.99 % Favored : 91.81 % Rotamer: Outliers : 5.60 % Allowed : 24.43 % Favored : 69.97 % 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: 0.66 (0.40), residues: 513 helix: 1.63 (0.29), residues: 354 sheet: None (None), residues: 0 loop : -2.46 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 24 HIS 0.001 0.000 HIS A 209 PHE 0.013 0.001 PHE A 368 TYR 0.013 0.001 TYR A 175 ARG 0.005 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.423 Fit side-chains outliers start: 22 outliers final: 15 residues processed: 100 average time/residue: 0.1542 time to fit residues: 19.4547 Evaluate side-chains 94 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 490 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4065 Z= 0.181 Angle : 0.610 7.678 5562 Z= 0.308 Chirality : 0.042 0.172 652 Planarity : 0.004 0.034 674 Dihedral : 11.580 72.987 650 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.59 % Rotamer: Outliers : 5.85 % Allowed : 26.97 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.40), residues: 513 helix: 1.69 (0.29), residues: 354 sheet: None (None), residues: 0 loop : -2.32 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 24 HIS 0.001 0.000 HIS A 4 PHE 0.010 0.001 PHE A 244 TYR 0.013 0.001 TYR A 111 ARG 0.004 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.319 Fit side-chains outliers start: 23 outliers final: 19 residues processed: 98 average time/residue: 0.1183 time to fit residues: 14.7158 Evaluate side-chains 98 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 490 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 0.0170 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4065 Z= 0.178 Angle : 0.603 7.672 5562 Z= 0.304 Chirality : 0.041 0.143 652 Planarity : 0.004 0.035 674 Dihedral : 9.550 59.815 650 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.99 % Favored : 91.81 % Rotamer: Outliers : 7.38 % Allowed : 26.46 % Favored : 66.16 % 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: 0.78 (0.40), residues: 513 helix: 1.67 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -2.30 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 24 HIS 0.001 0.000 HIS A 209 PHE 0.008 0.001 PHE A 244 TYR 0.009 0.001 TYR A 111 ARG 0.005 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.430 Fit side-chains REVERT: A 4 HIS cc_start: 0.5176 (OUTLIER) cc_final: 0.3827 (m-70) outliers start: 29 outliers final: 20 residues processed: 99 average time/residue: 0.1579 time to fit residues: 20.0785 Evaluate side-chains 105 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 490 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.0770 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4065 Z= 0.200 Angle : 0.611 7.700 5562 Z= 0.306 Chirality : 0.040 0.140 652 Planarity : 0.004 0.034 674 Dihedral : 8.047 44.505 650 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.82 % Favored : 92.98 % Rotamer: Outliers : 7.12 % Allowed : 27.99 % Favored : 64.89 % 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: 0.83 (0.40), residues: 513 helix: 1.71 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -2.28 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 24 HIS 0.001 0.000 HIS A 209 PHE 0.008 0.001 PHE A 244 TYR 0.013 0.001 TYR A 111 ARG 0.005 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.401 Fit side-chains REVERT: A 4 HIS cc_start: 0.5204 (OUTLIER) cc_final: 0.3849 (m-70) outliers start: 28 outliers final: 20 residues processed: 102 average time/residue: 0.1625 time to fit residues: 21.2402 Evaluate side-chains 105 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 490 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4065 Z= 0.293 Angle : 0.691 8.632 5562 Z= 0.350 Chirality : 0.043 0.155 652 Planarity : 0.005 0.049 674 Dihedral : 7.349 43.085 650 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.77 % Favored : 91.03 % Rotamer: Outliers : 7.12 % Allowed : 28.50 % Favored : 64.38 % 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: 0.48 (0.40), residues: 513 helix: 1.38 (0.29), residues: 361 sheet: None (None), residues: 0 loop : -2.37 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 24 HIS 0.002 0.001 HIS A 209 PHE 0.011 0.002 PHE A 244 TYR 0.013 0.002 TYR A 175 ARG 0.005 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.406 Fit side-chains REVERT: A 4 HIS cc_start: 0.5341 (OUTLIER) cc_final: 0.4786 (m-70) outliers start: 28 outliers final: 23 residues processed: 99 average time/residue: 0.1641 time to fit residues: 20.8345 Evaluate side-chains 106 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 490 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4065 Z= 0.185 Angle : 0.617 7.710 5562 Z= 0.307 Chirality : 0.040 0.153 652 Planarity : 0.004 0.034 674 Dihedral : 6.334 38.642 650 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.24 % Favored : 93.57 % Rotamer: Outliers : 5.34 % Allowed : 30.53 % Favored : 64.12 % 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: 0.78 (0.40), residues: 513 helix: 1.68 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -2.32 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 228 HIS 0.000 0.000 HIS A 162 PHE 0.007 0.001 PHE A 244 TYR 0.011 0.001 TYR A 111 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.904 Fit side-chains REVERT: A 4 HIS cc_start: 0.5313 (OUTLIER) cc_final: 0.3931 (m-70) outliers start: 21 outliers final: 17 residues processed: 98 average time/residue: 0.1644 time to fit residues: 20.5332 Evaluate side-chains 97 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 428 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4065 Z= 0.221 Angle : 0.662 9.110 5562 Z= 0.327 Chirality : 0.042 0.234 652 Planarity : 0.004 0.043 674 Dihedral : 6.236 40.126 650 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.99 % Favored : 91.81 % Rotamer: Outliers : 4.07 % Allowed : 31.81 % Favored : 64.12 % 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: 0.68 (0.40), residues: 513 helix: 1.60 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -2.34 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 228 HIS 0.001 0.000 HIS A 209 PHE 0.008 0.001 PHE A 101 TYR 0.016 0.001 TYR A 111 ARG 0.005 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.433 Fit side-chains REVERT: A 4 HIS cc_start: 0.5376 (OUTLIER) cc_final: 0.4773 (m-70) outliers start: 16 outliers final: 14 residues processed: 89 average time/residue: 0.1707 time to fit residues: 19.0029 Evaluate side-chains 97 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 428 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 50 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4065 Z= 0.209 Angle : 0.658 8.981 5562 Z= 0.326 Chirality : 0.042 0.215 652 Planarity : 0.004 0.042 674 Dihedral : 5.987 39.754 650 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.02 % Favored : 92.79 % Rotamer: Outliers : 4.83 % Allowed : 31.55 % Favored : 63.61 % 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: 0.67 (0.40), residues: 513 helix: 1.62 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -2.42 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 228 HIS 0.001 0.000 HIS A 209 PHE 0.009 0.001 PHE A 140 TYR 0.013 0.001 TYR A 175 ARG 0.007 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.420 Fit side-chains REVERT: A 4 HIS cc_start: 0.5345 (OUTLIER) cc_final: 0.4764 (m-70) outliers start: 19 outliers final: 15 residues processed: 93 average time/residue: 0.1568 time to fit residues: 18.2311 Evaluate side-chains 96 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 428 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4065 Z= 0.259 Angle : 0.686 8.005 5562 Z= 0.345 Chirality : 0.043 0.239 652 Planarity : 0.005 0.055 674 Dihedral : 6.235 42.162 650 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.38 % Favored : 91.42 % Rotamer: Outliers : 4.07 % Allowed : 31.30 % Favored : 64.63 % 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: 0.47 (0.40), residues: 513 helix: 1.46 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -2.46 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 228 HIS 0.002 0.001 HIS A 209 PHE 0.011 0.001 PHE A 244 TYR 0.016 0.002 TYR A 175 ARG 0.007 0.001 ARG A 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.428 Fit side-chains REVERT: A 4 HIS cc_start: 0.5557 (OUTLIER) cc_final: 0.4971 (m-70) outliers start: 16 outliers final: 14 residues processed: 89 average time/residue: 0.1608 time to fit residues: 17.9414 Evaluate side-chains 96 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 428 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** 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 = 0.4232 r_free = 0.4232 target = 0.197205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.183139 restraints weight = 6235.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.186600 restraints weight = 3535.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.188865 restraints weight = 2281.175| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4065 Z= 0.207 Angle : 0.660 8.061 5562 Z= 0.329 Chirality : 0.042 0.234 652 Planarity : 0.004 0.041 674 Dihedral : 5.906 40.200 650 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.43 % Favored : 93.37 % Rotamer: Outliers : 5.34 % Allowed : 30.03 % Favored : 64.63 % 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: 0.59 (0.40), residues: 513 helix: 1.55 (0.29), residues: 355 sheet: None (None), residues: 0 loop : -2.44 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 228 HIS 0.001 0.000 HIS A 4 PHE 0.009 0.001 PHE A 244 TYR 0.013 0.001 TYR A 175 ARG 0.008 0.001 ARG A 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1211.98 seconds wall clock time: 28 minutes 23.36 seconds (1703.36 seconds total)