Starting phenix.real_space_refine on Tue Mar 11 23:23:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ijz_60646/03_2025/9ijz_60646_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ijz_60646/03_2025/9ijz_60646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ijz_60646/03_2025/9ijz_60646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ijz_60646/03_2025/9ijz_60646.map" model { file = "/net/cci-nas-00/data/ceres_data/9ijz_60646/03_2025/9ijz_60646_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ijz_60646/03_2025/9ijz_60646_trim.cif" } resolution = 2.91 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= 0.000 sd= 0.058 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 P 4 5.49 5 S 32 5.16 5 C 4474 2.51 5 N 1054 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6654 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3270 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 13, 'TRANS': 378} Chain breaks: 1 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'6PL': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 5.96, per 1000 atoms: 0.90 Number of scatterers: 6654 At special positions: 0 Unit cell: (69.9, 123.956, 77.356, 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) S 32 16.00 P 4 15.00 O 1090 8.00 N 1054 7.00 C 4474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.03 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: 1.84 Conformation dependent library (CDL) restraints added in 867.9 milliseconds 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 77.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 230 through 257 Processing helix chain 'A' and resid 265 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 312 through 336 Processing helix chain 'A' and resid 345 through 361 removed outlier: 3.802A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.591A pdb=" N PHE A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 403 through 420 removed outlier: 3.757A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 470 Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 472 through 503 removed outlier: 4.130A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 532 removed outlier: 4.403A pdb=" N VAL A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 571 removed outlier: 4.104A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 removed outlier: 3.820A pdb=" N ILE A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 618 Proline residue: A 598 - end of helix removed outlier: 3.835A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 257 Processing helix chain 'B' and resid 265 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 312 through 336 Processing helix chain 'B' and resid 345 through 361 removed outlier: 3.802A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 removed outlier: 3.591A pdb=" N PHE B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.757A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 470 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 472 through 503 removed outlier: 4.130A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 532 removed outlier: 4.403A pdb=" N VAL B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 571 removed outlier: 4.104A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 583 removed outlier: 3.820A pdb=" N ILE B 575 " --> pdb=" O PHE B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 618 Proline residue: B 598 - end of helix removed outlier: 3.835A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1374 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: 1.72 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 946 1.31 - 1.43: 2116 1.43 - 1.56: 3756 1.56 - 1.68: 4 1.68 - 1.81: 44 Bond restraints: 6866 Sorted by residual: bond pdb=" C11 6PL A1002 " pdb=" O3 6PL A1002 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C11 6PL B1002 " pdb=" O3 6PL B1002 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C31 6PL B1002 " pdb=" O2 6PL B1002 " ideal model delta sigma weight residual 1.330 1.416 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C31 6PL A1002 " pdb=" O2 6PL A1002 " ideal model delta sigma weight residual 1.330 1.416 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" CA TYR B 524 " pdb=" C TYR B 524 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.29e-02 6.01e+03 1.69e+01 ... (remaining 6861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 9252 3.78 - 7.56: 58 7.56 - 11.34: 4 11.34 - 15.12: 0 15.12 - 18.90: 4 Bond angle restraints: 9318 Sorted by residual: angle pdb=" O1P 6PL A1002 " pdb=" P 6PL A1002 " pdb=" O2P 6PL A1002 " ideal model delta sigma weight residual 119.71 100.81 18.90 3.00e+00 1.11e-01 3.97e+01 angle pdb=" O1P 6PL B1002 " pdb=" P 6PL B1002 " pdb=" O2P 6PL B1002 " ideal model delta sigma weight residual 119.71 100.81 18.90 3.00e+00 1.11e-01 3.97e+01 angle pdb=" O3P 6PL A1002 " pdb=" P 6PL A1002 " pdb=" O4P 6PL A1002 " ideal model delta sigma weight residual 93.65 110.78 -17.13 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O3P 6PL B1002 " pdb=" P 6PL B1002 " pdb=" O4P 6PL B1002 " ideal model delta sigma weight residual 93.65 110.78 -17.13 3.00e+00 1.11e-01 3.26e+01 angle pdb=" CA GLU B 549 " pdb=" CB GLU B 549 " pdb=" CG GLU B 549 " ideal model delta sigma weight residual 114.10 121.53 -7.43 2.00e+00 2.50e-01 1.38e+01 ... (remaining 9313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.77: 3262 14.77 - 29.53: 444 29.53 - 44.30: 146 44.30 - 59.07: 64 59.07 - 73.83: 4 Dihedral angle restraints: 3920 sinusoidal: 1610 harmonic: 2310 Sorted by residual: dihedral pdb=" CA PRO B 475 " pdb=" C PRO B 475 " pdb=" N HIS B 476 " pdb=" CA HIS B 476 " ideal model delta harmonic sigma weight residual -180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA PRO A 475 " pdb=" C PRO A 475 " pdb=" N HIS A 476 " pdb=" CA HIS A 476 " ideal model delta harmonic sigma weight residual -180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA GLY A 621 " pdb=" C GLY A 621 " pdb=" N GLU A 622 " pdb=" CA GLU A 622 " ideal model delta harmonic sigma weight residual -180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 3917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 708 0.037 - 0.074: 234 0.074 - 0.112: 54 0.112 - 0.149: 8 0.149 - 0.186: 2 Chirality restraints: 1006 Sorted by residual: chirality pdb=" C2 6PL A1002 " pdb=" C1 6PL A1002 " pdb=" C3 6PL A1002 " pdb=" O2 6PL A1002 " both_signs ideal model delta sigma weight residual False -2.33 -2.51 0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" C2 6PL B1002 " pdb=" C1 6PL B1002 " pdb=" C3 6PL B1002 " pdb=" O2 6PL B1002 " both_signs ideal model delta sigma weight residual False -2.33 -2.51 0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" CA GLU A 549 " pdb=" N GLU A 549 " pdb=" C GLU A 549 " pdb=" CB GLU A 549 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 1003 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 523 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C CYS B 523 " 0.042 2.00e-02 2.50e+03 pdb=" O CYS B 523 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR B 524 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 523 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C CYS A 523 " -0.042 2.00e-02 2.50e+03 pdb=" O CYS A 523 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 524 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 394 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C PHE B 394 " 0.035 2.00e-02 2.50e+03 pdb=" O PHE B 394 " -0.013 2.00e-02 2.50e+03 pdb=" N TRP B 395 " -0.012 2.00e-02 2.50e+03 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 78 2.61 - 3.18: 6004 3.18 - 3.75: 10815 3.75 - 4.33: 14931 4.33 - 4.90: 24260 Nonbonded interactions: 56088 Sorted by model distance: nonbonded pdb=" O PHE A 366 " pdb=" NH1 ARG A 371 " model vdw 2.034 3.120 nonbonded pdb=" O PHE B 366 " pdb=" NH1 ARG B 371 " model vdw 2.034 3.120 nonbonded pdb=" O LYS A 482 " pdb=" OG1 THR A 485 " model vdw 2.193 3.040 nonbonded pdb=" O LYS B 482 " pdb=" OG1 THR B 485 " model vdw 2.193 3.040 nonbonded pdb=" O ILE B 579 " pdb=" OG1 THR B 583 " model vdw 2.206 3.040 ... (remaining 56083 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.620 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.260 Find NCS groups from input model: 0.120 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:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 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 : 0.006 0.103 6866 Z= 0.372 Angle : 0.788 18.904 9318 Z= 0.363 Chirality : 0.040 0.186 1006 Planarity : 0.004 0.024 1122 Dihedral : 16.399 73.832 2426 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.29 % Allowed : 25.36 % Favored : 74.35 % 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: 0.55 (0.29), residues: 776 helix: 1.12 (0.20), residues: 554 sheet: None (None), residues: 0 loop : -1.53 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 373 HIS 0.002 0.001 HIS A 476 PHE 0.011 0.001 PHE A 610 TYR 0.014 0.001 TYR A 524 ARG 0.003 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.754 Fit side-chains REVERT: A 511 PHE cc_start: 0.9074 (t80) cc_final: 0.8849 (t80) REVERT: B 511 PHE cc_start: 0.9073 (t80) cc_final: 0.8849 (t80) outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.8001 time to fit residues: 90.1123 Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 452 GLN B 248 ASN B 452 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.183596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.148145 restraints weight = 8479.595| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.30 r_work: 0.3611 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6866 Z= 0.195 Angle : 0.551 5.578 9318 Z= 0.299 Chirality : 0.040 0.127 1006 Planarity : 0.004 0.027 1122 Dihedral : 10.504 80.693 960 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.59 % Allowed : 22.48 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.30), residues: 776 helix: 1.62 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.79 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 232 HIS 0.002 0.001 HIS A 476 PHE 0.017 0.002 PHE B 257 TYR 0.012 0.002 TYR B 352 ARG 0.004 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.702 Fit side-chains REVERT: A 511 PHE cc_start: 0.9077 (t80) cc_final: 0.8812 (t80) REVERT: B 511 PHE cc_start: 0.9077 (t80) cc_final: 0.8814 (t80) outliers start: 18 outliers final: 8 residues processed: 114 average time/residue: 0.7374 time to fit residues: 91.4392 Evaluate side-chains 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 408 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 0.0970 chunk 66 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.182457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.144983 restraints weight = 8453.756| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.48 r_work: 0.3569 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6866 Z= 0.198 Angle : 0.532 5.557 9318 Z= 0.288 Chirality : 0.040 0.129 1006 Planarity : 0.003 0.027 1122 Dihedral : 10.127 73.784 960 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.75 % Allowed : 20.17 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.30), residues: 776 helix: 1.71 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -1.82 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 232 HIS 0.002 0.001 HIS B 313 PHE 0.015 0.002 PHE A 391 TYR 0.010 0.001 TYR B 467 ARG 0.002 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.765 Fit side-chains REVERT: A 511 PHE cc_start: 0.9089 (t80) cc_final: 0.8859 (t80) REVERT: B 511 PHE cc_start: 0.9088 (t80) cc_final: 0.8860 (t80) outliers start: 26 outliers final: 16 residues processed: 124 average time/residue: 0.7741 time to fit residues: 103.9629 Evaluate side-chains 114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 447 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.180538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144139 restraints weight = 8608.194| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.42 r_work: 0.3551 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6866 Z= 0.234 Angle : 0.558 5.620 9318 Z= 0.303 Chirality : 0.041 0.128 1006 Planarity : 0.004 0.030 1122 Dihedral : 10.156 71.236 960 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.90 % Allowed : 20.46 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.30), residues: 776 helix: 1.67 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -1.86 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 232 HIS 0.002 0.001 HIS A 313 PHE 0.018 0.002 PHE A 391 TYR 0.012 0.002 TYR B 467 ARG 0.002 0.000 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.7932 (t) REVERT: A 511 PHE cc_start: 0.9072 (t80) cc_final: 0.8846 (t80) REVERT: A 549 GLU cc_start: 0.7783 (pp20) cc_final: 0.7533 (pp20) REVERT: B 261 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.7931 (t) REVERT: B 511 PHE cc_start: 0.9074 (t80) cc_final: 0.8849 (t80) REVERT: B 549 GLU cc_start: 0.7785 (pp20) cc_final: 0.7536 (pp20) outliers start: 34 outliers final: 20 residues processed: 130 average time/residue: 0.7710 time to fit residues: 108.3279 Evaluate side-chains 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 489 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.181235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144388 restraints weight = 8650.294| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.46 r_work: 0.3579 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6866 Z= 0.198 Angle : 0.550 5.506 9318 Z= 0.301 Chirality : 0.040 0.131 1006 Planarity : 0.003 0.031 1122 Dihedral : 10.020 67.182 960 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.32 % Allowed : 19.88 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.29), residues: 776 helix: 1.73 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -1.84 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.002 0.001 HIS B 313 PHE 0.018 0.001 PHE A 391 TYR 0.013 0.002 TYR A 352 ARG 0.002 0.000 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 499 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.7920 (m-70) REVERT: A 511 PHE cc_start: 0.9078 (t80) cc_final: 0.8833 (t80) REVERT: B 499 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.7927 (m-70) REVERT: B 511 PHE cc_start: 0.9079 (t80) cc_final: 0.8835 (t80) outliers start: 30 outliers final: 18 residues processed: 130 average time/residue: 0.8031 time to fit residues: 112.5689 Evaluate side-chains 122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 499 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 7.9990 chunk 75 optimal weight: 0.0010 chunk 55 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 294 GLN B 248 ASN B 294 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.180457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144184 restraints weight = 8466.584| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.40 r_work: 0.3568 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6866 Z= 0.211 Angle : 0.567 6.778 9318 Z= 0.306 Chirality : 0.040 0.132 1006 Planarity : 0.004 0.032 1122 Dihedral : 9.660 63.592 960 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.90 % Allowed : 19.60 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.30), residues: 776 helix: 1.74 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -1.79 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 327 HIS 0.002 0.001 HIS A 313 PHE 0.019 0.002 PHE A 391 TYR 0.013 0.002 TYR A 352 ARG 0.002 0.000 ARG A 448 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.697 Fit side-chains REVERT: A 261 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.7925 (t) REVERT: A 448 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7359 (ttm110) REVERT: A 511 PHE cc_start: 0.9063 (t80) cc_final: 0.8851 (t80) REVERT: B 261 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.7929 (t) REVERT: B 448 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7366 (ttm110) REVERT: B 511 PHE cc_start: 0.9066 (t80) cc_final: 0.8854 (t80) outliers start: 34 outliers final: 16 residues processed: 128 average time/residue: 0.7313 time to fit residues: 101.3282 Evaluate side-chains 118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 552 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 0.0070 chunk 64 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.181190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144864 restraints weight = 8552.415| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.41 r_work: 0.3572 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6866 Z= 0.194 Angle : 0.561 6.377 9318 Z= 0.303 Chirality : 0.041 0.132 1006 Planarity : 0.004 0.032 1122 Dihedral : 9.240 57.220 960 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.32 % Allowed : 20.75 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.29), residues: 776 helix: 1.70 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -1.71 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.002 0.001 HIS A 313 PHE 0.018 0.001 PHE A 391 TYR 0.014 0.002 TYR B 352 ARG 0.006 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 477 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8127 (mm) REVERT: A 499 HIS cc_start: 0.8288 (OUTLIER) cc_final: 0.7921 (m-70) REVERT: A 511 PHE cc_start: 0.9036 (t80) cc_final: 0.8817 (t80) REVERT: A 532 MET cc_start: 0.7605 (mmp) cc_final: 0.7258 (mmm) REVERT: A 533 ASP cc_start: 0.7407 (m-30) cc_final: 0.7095 (t0) REVERT: B 477 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8140 (mm) REVERT: B 499 HIS cc_start: 0.8294 (OUTLIER) cc_final: 0.7930 (m-70) REVERT: B 511 PHE cc_start: 0.9037 (t80) cc_final: 0.8820 (t80) REVERT: B 532 MET cc_start: 0.7623 (mmp) cc_final: 0.7275 (mmm) REVERT: B 533 ASP cc_start: 0.7403 (m-30) cc_final: 0.7101 (t0) outliers start: 30 outliers final: 20 residues processed: 122 average time/residue: 0.6905 time to fit residues: 91.7988 Evaluate side-chains 122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 552 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN B 294 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.180721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143997 restraints weight = 8664.464| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.44 r_work: 0.3574 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6866 Z= 0.213 Angle : 0.570 6.341 9318 Z= 0.309 Chirality : 0.041 0.146 1006 Planarity : 0.004 0.032 1122 Dihedral : 8.802 53.191 960 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.47 % Allowed : 20.32 % Favored : 75.22 % 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: 1.21 (0.29), residues: 776 helix: 1.68 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.67 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 327 HIS 0.002 0.001 HIS A 313 PHE 0.017 0.002 PHE A 391 TYR 0.013 0.002 TYR A 352 ARG 0.005 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.7925 (t) REVERT: A 377 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6412 (tp) REVERT: A 477 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8123 (mm) REVERT: A 532 MET cc_start: 0.7628 (mmp) cc_final: 0.7325 (mmm) REVERT: A 549 GLU cc_start: 0.7770 (pp20) cc_final: 0.7551 (pp20) REVERT: A 615 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: B 261 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.7927 (t) REVERT: B 377 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6395 (tp) REVERT: B 477 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8138 (mm) REVERT: B 532 MET cc_start: 0.7649 (mmp) cc_final: 0.7347 (mmm) REVERT: B 549 GLU cc_start: 0.7775 (pp20) cc_final: 0.7557 (pp20) REVERT: B 615 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7718 (mp0) outliers start: 31 outliers final: 16 residues processed: 125 average time/residue: 0.7740 time to fit residues: 104.3288 Evaluate side-chains 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 56 optimal weight: 0.2980 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 294 GLN B 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.181580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.145073 restraints weight = 8609.448| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.43 r_work: 0.3584 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6866 Z= 0.197 Angle : 0.569 6.201 9318 Z= 0.309 Chirality : 0.041 0.142 1006 Planarity : 0.004 0.032 1122 Dihedral : 8.511 50.917 960 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.89 % Allowed : 21.61 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.29), residues: 776 helix: 1.67 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.66 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 327 HIS 0.002 0.001 HIS B 313 PHE 0.017 0.001 PHE A 391 TYR 0.014 0.002 TYR B 352 ARG 0.005 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7909 (t) REVERT: A 377 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6337 (tp) REVERT: A 477 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8098 (mm) REVERT: A 499 HIS cc_start: 0.8303 (OUTLIER) cc_final: 0.7885 (m-70) REVERT: A 532 MET cc_start: 0.7579 (mmp) cc_final: 0.7277 (mmm) REVERT: A 533 ASP cc_start: 0.7510 (m-30) cc_final: 0.7194 (t0) REVERT: A 590 ASP cc_start: 0.8140 (m-30) cc_final: 0.7925 (m-30) REVERT: A 615 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: B 261 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7911 (t) REVERT: B 377 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6327 (tp) REVERT: B 477 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8106 (mm) REVERT: B 499 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.7898 (m-70) REVERT: B 532 MET cc_start: 0.7598 (mmp) cc_final: 0.7294 (mmm) REVERT: B 533 ASP cc_start: 0.7506 (m-30) cc_final: 0.7195 (t0) REVERT: B 590 ASP cc_start: 0.8143 (m-30) cc_final: 0.7924 (m-30) REVERT: B 615 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7707 (mp0) outliers start: 27 outliers final: 16 residues processed: 117 average time/residue: 0.7735 time to fit residues: 98.4298 Evaluate side-chains 122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.180157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143340 restraints weight = 8770.282| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.47 r_work: 0.3579 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6866 Z= 0.223 Angle : 0.583 6.208 9318 Z= 0.316 Chirality : 0.042 0.149 1006 Planarity : 0.004 0.033 1122 Dihedral : 8.365 47.946 960 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.75 % Allowed : 21.90 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.29), residues: 776 helix: 1.64 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.64 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 327 HIS 0.002 0.001 HIS A 313 PHE 0.018 0.002 PHE B 391 TYR 0.014 0.002 TYR A 290 ARG 0.005 0.000 ARG B 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6446 (tp) REVERT: A 477 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8133 (mm) REVERT: A 499 HIS cc_start: 0.8277 (OUTLIER) cc_final: 0.7880 (m-70) REVERT: A 532 MET cc_start: 0.7609 (mmp) cc_final: 0.7331 (mmm) REVERT: A 590 ASP cc_start: 0.8171 (m-30) cc_final: 0.7953 (m-30) REVERT: B 377 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6435 (tp) REVERT: B 477 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8156 (mm) REVERT: B 499 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.7893 (m-70) REVERT: B 532 MET cc_start: 0.7642 (mmp) cc_final: 0.7364 (mmm) REVERT: B 590 ASP cc_start: 0.8167 (m-30) cc_final: 0.7948 (m-30) outliers start: 26 outliers final: 14 residues processed: 118 average time/residue: 0.6881 time to fit residues: 88.3153 Evaluate side-chains 120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 552 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 52 optimal weight: 0.0030 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 0.0070 chunk 61 optimal weight: 0.8980 overall best weight: 0.3408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.183561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147796 restraints weight = 8680.810| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.38 r_work: 0.3605 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6866 Z= 0.174 Angle : 0.571 6.576 9318 Z= 0.310 Chirality : 0.041 0.136 1006 Planarity : 0.003 0.032 1122 Dihedral : 8.019 46.222 960 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.59 % Allowed : 23.34 % Favored : 74.06 % 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: 1.33 (0.29), residues: 776 helix: 1.79 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.69 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 327 HIS 0.002 0.001 HIS B 476 PHE 0.017 0.001 PHE A 391 TYR 0.014 0.002 TYR A 352 ARG 0.005 0.000 ARG A 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3999.46 seconds wall clock time: 69 minutes 2.48 seconds (4142.48 seconds total)