Starting phenix.real_space_refine on Wed Mar 5 20:42:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9irx_60824/03_2025/9irx_60824.cif Found real_map, /net/cci-nas-00/data/ceres_data/9irx_60824/03_2025/9irx_60824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9irx_60824/03_2025/9irx_60824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9irx_60824/03_2025/9irx_60824.map" model { file = "/net/cci-nas-00/data/ceres_data/9irx_60824/03_2025/9irx_60824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9irx_60824/03_2025/9irx_60824.cif" } resolution = 3.0 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= -0.002 sd= 0.143 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: 5 Type Number sf(0) Gaussians Br 2 7.06 5 S 27 5.16 5 C 2305 2.51 5 N 586 2.21 5 O 589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3509 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3487 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 26, 'TRANS': 442} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'R75': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.97, per 1000 atoms: 0.85 Number of scatterers: 3509 At special positions: 0 Unit cell: (106.7, 55.484, 66.154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 2 34.99 S 27 16.00 O 589 8.00 N 586 7.00 C 2305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " distance=2.02 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 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 453.1 milliseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 856 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 82.1% alpha, 1.3% 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 3 through 11 Processing helix chain 'A' and resid 14 through 37 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.504A pdb=" N SER A 141 " --> pdb=" O VAL A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 170 removed outlier: 3.626A pdb=" N LEU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 171 through 192 Processing helix chain 'A' and resid 195 through 223 removed outlier: 3.603A pdb=" N GLY A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 229 through 255 removed outlier: 3.506A pdb=" N PHE A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 267 through 276 removed outlier: 4.034A pdb=" N LEU A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 316 through 324 removed outlier: 3.549A pdb=" N LEU A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 368 Processing helix chain 'A' and resid 377 through 403 removed outlier: 3.733A pdb=" N GLY A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Proline residue: A 391 - end of helix removed outlier: 4.011A pdb=" N SER A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 426 Processing helix chain 'A' and resid 430 through 456 Processing helix chain 'A' and resid 464 through 486 Proline residue: A 484 - end of helix Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.563A pdb=" N VAL A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 removed outlier: 4.199A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 513 through 515 No H-bonds generated for 'chain 'A' and resid 513 through 515' Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 266 hydrogen bonds defined for protein. 786 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: 1.03 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 803 1.33 - 1.48: 1220 1.48 - 1.64: 1526 1.64 - 1.79: 0 1.79 - 1.94: 44 Bond restraints: 3593 Sorted by residual: bond pdb=" CAO R75 A 601 " pdb=" CAS R75 A 601 " ideal model delta sigma weight residual 1.382 1.571 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" CAP R75 A 601 " pdb=" CAV R75 A 601 " ideal model delta sigma weight residual 1.396 1.569 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" CAD R75 A 601 " pdb=" CAE R75 A 601 " ideal model delta sigma weight residual 1.382 1.528 -0.146 2.00e-02 2.50e+03 5.31e+01 bond pdb=" CAA R75 A 601 " pdb=" CAB R75 A 601 " ideal model delta sigma weight residual 1.378 1.519 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" CAC R75 A 601 " pdb=" CAD R75 A 601 " ideal model delta sigma weight residual 1.400 1.533 -0.133 2.00e-02 2.50e+03 4.46e+01 ... (remaining 3588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4808 1.56 - 3.12: 61 3.12 - 4.68: 28 4.68 - 6.24: 4 6.24 - 7.80: 5 Bond angle restraints: 4906 Sorted by residual: angle pdb=" CAJ R75 A 601 " pdb=" CAL R75 A 601 " pdb=" CAP R75 A 601 " ideal model delta sigma weight residual 129.37 121.57 7.80 3.00e+00 1.11e-01 6.76e+00 angle pdb=" CAQ R75 A 601 " pdb=" CAM R75 A 601 " pdb=" OAN R75 A 601 " ideal model delta sigma weight residual 116.30 124.01 -7.71 3.00e+00 1.11e-01 6.61e+00 angle pdb=" C VAL A 162 " pdb=" CA VAL A 162 " pdb=" CB VAL A 162 " ideal model delta sigma weight residual 111.94 108.87 3.07 1.26e+00 6.30e-01 5.92e+00 angle pdb=" CAS R75 A 601 " pdb=" CAO R75 A 601 " pdb=" OAN R75 A 601 " ideal model delta sigma weight residual 125.82 132.61 -6.79 3.00e+00 1.11e-01 5.13e+00 angle pdb=" CA TYR A 275 " pdb=" CB TYR A 275 " pdb=" CG TYR A 275 " ideal model delta sigma weight residual 113.90 117.90 -4.00 1.80e+00 3.09e-01 4.95e+00 ... (remaining 4901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.60: 2043 27.60 - 55.19: 37 55.19 - 82.79: 4 82.79 - 110.39: 0 110.39 - 137.99: 1 Dihedral angle restraints: 2085 sinusoidal: 758 harmonic: 1327 Sorted by residual: dihedral pdb=" CAL R75 A 601 " pdb=" CAM R75 A 601 " pdb=" CAQ R75 A 601 " pdb=" CAR R75 A 601 " ideal model delta sinusoidal sigma weight residual 263.96 125.97 137.99 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" SG CYS A 49 " pdb=" CB CYS A 116 " pdb=" SG CYS A 116 " pdb=" CA CYS A 116 " ideal model delta sinusoidal sigma weight residual 79.00 26.30 52.70 1 2.00e+01 2.50e-03 9.46e+00 dihedral pdb=" N LEU A 437 " pdb=" CA LEU A 437 " pdb=" CB LEU A 437 " pdb=" CG LEU A 437 " ideal model delta sinusoidal sigma weight residual -60.00 -110.18 50.18 3 1.50e+01 4.44e-03 8.87e+00 ... (remaining 2082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 381 0.026 - 0.051: 137 0.051 - 0.077: 42 0.077 - 0.102: 25 0.102 - 0.128: 8 Chirality restraints: 593 Sorted by residual: chirality pdb=" CA ILE A 77 " pdb=" N ILE A 77 " pdb=" C ILE A 77 " pdb=" CB ILE A 77 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CB VAL A 210 " pdb=" CA VAL A 210 " pdb=" CG1 VAL A 210 " pdb=" CG2 VAL A 210 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA VAL A 121 " pdb=" N VAL A 121 " pdb=" C VAL A 121 " pdb=" CB VAL A 121 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 590 not shown) Planarity restraints: 598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 275 " 0.008 2.00e-02 2.50e+03 7.55e-03 1.14e+00 pdb=" CG TYR A 275 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 275 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 275 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 275 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 275 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 275 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 275 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 51 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 52 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 44 " -0.016 5.00e-02 4.00e+02 2.47e-02 9.79e-01 pdb=" N PRO A 45 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " -0.014 5.00e-02 4.00e+02 ... (remaining 595 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 371 2.74 - 3.28: 3735 3.28 - 3.82: 6332 3.82 - 4.36: 7404 4.36 - 4.90: 12697 Nonbonded interactions: 30539 Sorted by model distance: nonbonded pdb=" OE1 GLN A 149 " pdb=" NH2 ARG A 487 " model vdw 2.197 3.120 nonbonded pdb=" NH2 ARG A 349 " pdb=" O LEU A 459 " model vdw 2.237 3.120 nonbonded pdb=" O ALA A 335 " pdb=" OG1 THR A 467 " model vdw 2.259 3.040 nonbonded pdb=" NH1 ARG A 173 " pdb=" O LEU A 279 " model vdw 2.282 3.120 nonbonded pdb=" N GLU A 281 " pdb=" OE2 GLU A 298 " model vdw 2.285 3.120 ... (remaining 30534 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.040 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:13.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.189 3593 Z= 0.552 Angle : 0.581 7.803 4906 Z= 0.274 Chirality : 0.035 0.128 593 Planarity : 0.003 0.026 598 Dihedral : 11.281 137.986 1223 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.56 % Allowed : 3.89 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.40), residues: 457 helix: 1.76 (0.28), residues: 348 sheet: None (None), residues: 0 loop : 0.96 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 357 HIS 0.002 0.001 HIS A 47 PHE 0.012 0.001 PHE A 360 TYR 0.018 0.002 TYR A 275 ARG 0.002 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.320 Fit side-chains REVERT: A 37 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8253 (tp) outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.8489 time to fit residues: 53.1081 Evaluate side-chains 47 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 210 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.143773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116487 restraints weight = 2990.962| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.36 r_work: 0.3060 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 3593 Z= 0.305 Angle : 0.637 6.430 4906 Z= 0.308 Chirality : 0.041 0.198 593 Planarity : 0.004 0.031 598 Dihedral : 8.053 118.721 501 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.44 % Allowed : 7.78 % Favored : 87.78 % 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: 2.31 (0.40), residues: 457 helix: 1.69 (0.28), residues: 352 sheet: None (None), residues: 0 loop : 1.27 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 357 HIS 0.002 0.001 HIS A 245 PHE 0.015 0.002 PHE A 360 TYR 0.017 0.002 TYR A 275 ARG 0.005 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.397 Fit side-chains REVERT: A 37 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8467 (tp) REVERT: A 222 MET cc_start: 0.7032 (mmt) cc_final: 0.6816 (mmt) REVERT: A 430 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.5768 (mmt) outliers start: 16 outliers final: 4 residues processed: 64 average time/residue: 0.9209 time to fit residues: 61.3949 Evaluate side-chains 50 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 262 GLN A 473 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.136869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.108362 restraints weight = 3096.094| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.44 r_work: 0.3036 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3593 Z= 0.252 Angle : 0.600 6.483 4906 Z= 0.288 Chirality : 0.039 0.178 593 Planarity : 0.004 0.029 598 Dihedral : 7.797 107.850 501 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.06 % Allowed : 11.39 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.39), residues: 457 helix: 1.59 (0.27), residues: 352 sheet: None (None), residues: 0 loop : 1.18 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 357 HIS 0.002 0.001 HIS A 245 PHE 0.014 0.002 PHE A 360 TYR 0.016 0.002 TYR A 275 ARG 0.005 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.373 Fit side-chains REVERT: A 430 MET cc_start: 0.6496 (OUTLIER) cc_final: 0.5726 (mmt) outliers start: 11 outliers final: 5 residues processed: 57 average time/residue: 0.8949 time to fit residues: 53.3652 Evaluate side-chains 52 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 20 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.139977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112241 restraints weight = 3104.529| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.42 r_work: 0.3041 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3593 Z= 0.271 Angle : 0.609 7.666 4906 Z= 0.291 Chirality : 0.040 0.184 593 Planarity : 0.004 0.051 598 Dihedral : 7.689 99.359 501 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.61 % Allowed : 13.06 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.40), residues: 457 helix: 1.50 (0.27), residues: 358 sheet: None (None), residues: 0 loop : 1.38 (0.69), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 357 HIS 0.002 0.001 HIS A 245 PHE 0.014 0.002 PHE A 360 TYR 0.017 0.002 TYR A 275 ARG 0.013 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.347 Fit side-chains REVERT: A 430 MET cc_start: 0.6519 (OUTLIER) cc_final: 0.6316 (mmm) outliers start: 13 outliers final: 7 residues processed: 55 average time/residue: 0.8369 time to fit residues: 48.1420 Evaluate side-chains 54 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 chunk 30 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.139100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.110739 restraints weight = 3184.135| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.47 r_work: 0.3078 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3593 Z= 0.182 Angle : 0.562 6.830 4906 Z= 0.265 Chirality : 0.037 0.167 593 Planarity : 0.004 0.058 598 Dihedral : 7.336 83.405 501 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.61 % Allowed : 15.56 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.40), residues: 457 helix: 1.65 (0.27), residues: 360 sheet: None (None), residues: 0 loop : 1.27 (0.71), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 357 HIS 0.001 0.000 HIS A 245 PHE 0.013 0.002 PHE A 360 TYR 0.015 0.001 TYR A 275 ARG 0.013 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.382 Fit side-chains REVERT: A 278 TRP cc_start: 0.8115 (m100) cc_final: 0.7809 (m100) REVERT: A 300 ARG cc_start: 0.8360 (ttm110) cc_final: 0.8140 (ttm110) REVERT: A 388 VAL cc_start: 0.8379 (p) cc_final: 0.8019 (t) REVERT: A 430 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.5824 (mmt) outliers start: 13 outliers final: 5 residues processed: 60 average time/residue: 0.7355 time to fit residues: 46.4229 Evaluate side-chains 55 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.137221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.108319 restraints weight = 3229.033| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.50 r_work: 0.3046 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3593 Z= 0.244 Angle : 0.591 7.068 4906 Z= 0.280 Chirality : 0.040 0.237 593 Planarity : 0.004 0.045 598 Dihedral : 6.944 76.246 500 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.78 % Allowed : 17.50 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.40), residues: 457 helix: 1.69 (0.27), residues: 358 sheet: None (None), residues: 0 loop : 1.26 (0.69), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 357 HIS 0.002 0.001 HIS A 245 PHE 0.012 0.002 PHE A 362 TYR 0.017 0.002 TYR A 275 ARG 0.010 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.381 Fit side-chains REVERT: A 388 VAL cc_start: 0.8433 (p) cc_final: 0.8078 (t) outliers start: 10 outliers final: 5 residues processed: 53 average time/residue: 0.8421 time to fit residues: 47.0228 Evaluate side-chains 52 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 32 optimal weight: 0.0570 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 16 optimal weight: 0.0770 chunk 39 optimal weight: 0.5980 overall best weight: 0.3056 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.141014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.112639 restraints weight = 3143.653| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.45 r_work: 0.3091 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3593 Z= 0.180 Angle : 0.581 9.332 4906 Z= 0.271 Chirality : 0.038 0.184 593 Planarity : 0.005 0.070 598 Dihedral : 6.645 70.512 500 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.78 % Allowed : 18.06 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.40), residues: 457 helix: 1.74 (0.27), residues: 360 sheet: -1.62 (2.03), residues: 10 loop : 1.38 (0.74), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 357 HIS 0.001 0.000 HIS A 245 PHE 0.011 0.001 PHE A 362 TYR 0.014 0.001 TYR A 275 ARG 0.016 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.348 Fit side-chains REVERT: A 278 TRP cc_start: 0.8077 (m100) cc_final: 0.7783 (m100) REVERT: A 388 VAL cc_start: 0.8513 (p) cc_final: 0.8128 (t) outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 0.7750 time to fit residues: 44.9248 Evaluate side-chains 53 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 43 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.139177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.110702 restraints weight = 3174.739| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.46 r_work: 0.3036 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3593 Z= 0.232 Angle : 0.618 9.815 4906 Z= 0.286 Chirality : 0.040 0.236 593 Planarity : 0.005 0.070 598 Dihedral : 6.501 70.311 500 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.94 % Allowed : 19.44 % Favored : 78.61 % 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: 2.26 (0.40), residues: 457 helix: 1.71 (0.27), residues: 360 sheet: -1.68 (2.00), residues: 10 loop : 1.36 (0.74), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 357 HIS 0.005 0.001 HIS A 428 PHE 0.012 0.002 PHE A 362 TYR 0.019 0.002 TYR A 275 ARG 0.016 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.379 Fit side-chains REVERT: A 278 TRP cc_start: 0.8048 (m100) cc_final: 0.7749 (m100) REVERT: A 388 VAL cc_start: 0.8514 (p) cc_final: 0.8138 (t) outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.8578 time to fit residues: 45.8239 Evaluate side-chains 53 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 482 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.141254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.113073 restraints weight = 3095.305| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.43 r_work: 0.3058 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3593 Z= 0.222 Angle : 0.624 10.188 4906 Z= 0.289 Chirality : 0.040 0.237 593 Planarity : 0.005 0.074 598 Dihedral : 6.434 70.472 500 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.94 % Allowed : 19.44 % Favored : 78.61 % 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: 2.25 (0.40), residues: 457 helix: 1.71 (0.27), residues: 359 sheet: -1.67 (2.00), residues: 10 loop : 1.29 (0.73), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 357 HIS 0.005 0.001 HIS A 428 PHE 0.012 0.002 PHE A 362 TYR 0.014 0.002 TYR A 275 ARG 0.017 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.353 Fit side-chains REVERT: A 278 TRP cc_start: 0.8118 (m100) cc_final: 0.7816 (m100) REVERT: A 388 VAL cc_start: 0.8554 (p) cc_final: 0.8172 (t) outliers start: 7 outliers final: 6 residues processed: 53 average time/residue: 0.7907 time to fit residues: 43.9759 Evaluate side-chains 53 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.0670 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.142240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114174 restraints weight = 3173.294| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.45 r_work: 0.3063 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3593 Z= 0.205 Angle : 0.635 10.547 4906 Z= 0.293 Chirality : 0.040 0.237 593 Planarity : 0.005 0.076 598 Dihedral : 6.369 71.091 500 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.67 % Allowed : 20.28 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.40), residues: 457 helix: 1.69 (0.27), residues: 360 sheet: -1.70 (2.00), residues: 10 loop : 1.35 (0.74), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 357 HIS 0.005 0.001 HIS A 428 PHE 0.011 0.002 PHE A 362 TYR 0.022 0.002 TYR A 275 ARG 0.018 0.001 ARG A 300 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.341 Fit side-chains REVERT: A 278 TRP cc_start: 0.8088 (m100) cc_final: 0.7776 (m100) REVERT: A 388 VAL cc_start: 0.8560 (p) cc_final: 0.8191 (t) outliers start: 6 outliers final: 6 residues processed: 52 average time/residue: 0.8235 time to fit residues: 44.9174 Evaluate side-chains 56 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 482 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 6 optimal weight: 0.3980 chunk 31 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.139740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111446 restraints weight = 3192.947| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.46 r_work: 0.3063 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3593 Z= 0.201 Angle : 0.643 13.809 4906 Z= 0.294 Chirality : 0.040 0.258 593 Planarity : 0.004 0.062 598 Dihedral : 6.331 71.808 500 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.67 % Allowed : 21.11 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.40), residues: 457 helix: 1.70 (0.27), residues: 360 sheet: -1.70 (2.00), residues: 10 loop : 1.37 (0.74), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 357 HIS 0.005 0.001 HIS A 428 PHE 0.011 0.002 PHE A 362 TYR 0.015 0.002 TYR A 275 ARG 0.014 0.001 ARG A 300 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2613.81 seconds wall clock time: 45 minutes 24.06 seconds (2724.06 seconds total)