Starting phenix.real_space_refine on Tue Feb 11 23:46:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ijz_60646/02_2025/9ijz_60646_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ijz_60646/02_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_60646/02_2025/9ijz_60646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ijz_60646/02_2025/9ijz_60646.map" model { file = "/net/cci-nas-00/data/ceres_data/9ijz_60646/02_2025/9ijz_60646_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ijz_60646/02_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-5592/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: 6.02, 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 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: 1.85 Conformation dependent library (CDL) restraints added in 820.8 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: 0.45 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: 1.51 Time building geometry restraints manager: 2.10 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: 441 29.53 - 44.30: 146 44.30 - 59.07: 64 59.07 - 73.83: 4 Dihedral angle restraints: 3917 sinusoidal: 1607 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 3914 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 - 2.60: 77 2.60 - 3.18: 5978 3.18 - 3.75: 10807 3.75 - 4.33: 14945 4.33 - 4.90: 24284 Nonbonded interactions: 56091 Sorted by model distance: nonbonded pdb=" SG CYS B 415 " pdb=" SG CYS B 440 " model vdw 2.031 3.760 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 ... (remaining 56086 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: 1.900 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.890 Find NCS groups from input model: 0.110 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:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.930 ------------------------------------------------------------------------------- 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= 0.363 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 : 2.031 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 : 0.688 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: 0.7596 time to fit residues: 85.7213 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 : 0.747 ------------------------------------------------------------------------------- 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: 8.9990 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: 0.6378 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.181704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.145736 restraints weight = 8546.778| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.34 r_work: 0.3583 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6866 Z= 0.226 Angle : 0.569 5.720 9318 Z= 0.309 Chirality : 0.041 0.127 1006 Planarity : 0.004 0.027 1122 Dihedral : 10.610 82.194 960 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: 1.02 (0.30), residues: 776 helix: 1.56 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.78 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 232 HIS 0.003 0.001 HIS B 441 PHE 0.016 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 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.714 Fit side-chains REVERT: A 448 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7207 (ttp-110) REVERT: A 511 PHE cc_start: 0.9079 (t80) cc_final: 0.8816 (t80) REVERT: B 439 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8370 (tp) REVERT: B 448 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7235 (ttp-110) REVERT: B 511 PHE cc_start: 0.9078 (t80) cc_final: 0.8817 (t80) outliers start: 18 outliers final: 8 residues processed: 118 average time/residue: 0.7435 time to fit residues: 95.2256 Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 A residue 448 ARG 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 Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 448 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 65 optimal weight: 0.0770 chunk 24 optimal weight: 0.6980 chunk 51 optimal weight: 0.0870 chunk 66 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 overall best weight: 0.3716 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.183254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.146642 restraints weight = 8483.349| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.47 r_work: 0.3596 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6866 Z= 0.176 Angle : 0.525 5.494 9318 Z= 0.286 Chirality : 0.039 0.128 1006 Planarity : 0.003 0.028 1122 Dihedral : 10.081 73.629 960 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.75 % Allowed : 20.75 % 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 (0.29), residues: 776 helix: 1.75 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -1.81 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.001 0.001 HIS B 313 PHE 0.014 0.001 PHE A 391 TYR 0.012 0.001 TYR A 352 ARG 0.003 0.000 ARG B 448 *********************** 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 : 0.728 Fit side-chains REVERT: A 377 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6327 (tp) REVERT: A 511 PHE cc_start: 0.9088 (t80) cc_final: 0.8858 (t80) REVERT: B 377 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6319 (tp) REVERT: B 439 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8354 (tp) REVERT: B 511 PHE cc_start: 0.9088 (t80) cc_final: 0.8860 (t80) outliers start: 26 outliers final: 13 residues processed: 124 average time/residue: 0.7601 time to fit residues: 102.1278 Evaluate side-chains 116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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: 1.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 46 optimal weight: 0.0870 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 10.0000 overall best weight: 0.8960 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.178701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.142305 restraints weight = 8675.002| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.41 r_work: 0.3535 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6866 Z= 0.265 Angle : 0.573 5.645 9318 Z= 0.310 Chirality : 0.041 0.128 1006 Planarity : 0.004 0.031 1122 Dihedral : 10.246 72.963 960 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.90 % Allowed : 20.17 % 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: 1.10 (0.30), residues: 776 helix: 1.62 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -1.79 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 232 HIS 0.003 0.001 HIS A 313 PHE 0.019 0.002 PHE A 391 TYR 0.012 0.002 TYR A 559 ARG 0.002 0.000 ARG B 604 *********************** 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 142 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.685 Fit side-chains REVERT: A 511 PHE cc_start: 0.9074 (t80) cc_final: 0.8849 (t80) REVERT: A 549 GLU cc_start: 0.7755 (pp20) cc_final: 0.7501 (pp20) REVERT: B 439 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8335 (tp) REVERT: B 511 PHE cc_start: 0.9071 (t80) cc_final: 0.8849 (t80) REVERT: B 549 GLU cc_start: 0.7773 (pp20) cc_final: 0.7520 (pp20) outliers start: 34 outliers final: 17 residues processed: 132 average time/residue: 0.7862 time to fit residues: 111.9814 Evaluate side-chains 120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.8980 chunk 30 optimal weight: 0.0570 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.181227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.145346 restraints weight = 8651.385| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.38 r_work: 0.3582 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6866 Z= 0.202 Angle : 0.555 5.497 9318 Z= 0.303 Chirality : 0.040 0.131 1006 Planarity : 0.003 0.031 1122 Dihedral : 10.030 68.162 960 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.32 % Allowed : 20.61 % Favored : 75.07 % 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: 1.16 (0.30), residues: 776 helix: 1.67 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -1.77 (0.45), 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 0.002 PHE A 391 TYR 0.013 0.002 TYR A 352 ARG 0.003 0.000 ARG A 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 142 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.661 Fit side-chains REVERT: A 448 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7364 (ttp-110) REVERT: A 499 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.7924 (m-70) REVERT: A 511 PHE cc_start: 0.9080 (t80) cc_final: 0.8833 (t80) REVERT: B 377 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6420 (tp) REVERT: B 439 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8359 (tt) REVERT: B 448 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7413 (ttp-110) REVERT: B 499 HIS cc_start: 0.8283 (OUTLIER) cc_final: 0.7931 (m-70) REVERT: B 511 PHE cc_start: 0.9080 (t80) cc_final: 0.8833 (t80) outliers start: 30 outliers final: 14 residues processed: 128 average time/residue: 0.7489 time to fit residues: 104.4016 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 : 0.766 ------------------------------------------------------------------------------- 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 A residue 448 ARG 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 439 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 ARG 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: 0.5980 chunk 75 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.179977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.143794 restraints weight = 8511.989| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.39 r_work: 0.3561 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6866 Z= 0.223 Angle : 0.566 6.686 9318 Z= 0.306 Chirality : 0.041 0.131 1006 Planarity : 0.003 0.033 1122 Dihedral : 9.598 64.059 960 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.19 % Allowed : 19.74 % Favored : 75.07 % 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 (0.30), residues: 776 helix: 1.71 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.77 (0.45), 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 0.015 0.002 PHE A 257 TYR 0.013 0.002 TYR B 352 ARG 0.002 0.000 ARG B 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: 36 poor density : 102 time to evaluate : 0.712 Fit side-chains REVERT: A 448 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7421 (ttp-110) REVERT: A 499 HIS cc_start: 0.8258 (OUTLIER) cc_final: 0.7874 (m-70) REVERT: A 511 PHE cc_start: 0.9043 (t80) cc_final: 0.8830 (t80) REVERT: B 439 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8359 (tt) REVERT: B 448 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7433 (ttp-110) REVERT: B 499 HIS cc_start: 0.8270 (OUTLIER) cc_final: 0.7889 (m-70) REVERT: B 511 PHE cc_start: 0.9044 (t80) cc_final: 0.8831 (t80) outliers start: 36 outliers final: 17 residues processed: 126 average time/residue: 0.8064 time to fit residues: 109.4401 Evaluate side-chains 120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 498 THR Chi-restraints excluded: chain A residue 499 HIS 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 498 THR Chi-restraints excluded: chain B residue 499 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 3 optimal weight: 0.0670 chunk 64 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.4135 r_free = 0.4135 target = 0.181240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145242 restraints weight = 8608.992| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.37 r_work: 0.3575 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6866 Z= 0.196 Angle : 0.560 6.213 9318 Z= 0.304 Chirality : 0.040 0.133 1006 Planarity : 0.003 0.033 1122 Dihedral : 9.246 58.052 960 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.18 % Allowed : 21.04 % Favored : 74.78 % 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: 1.22 (0.30), residues: 776 helix: 1.71 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.74 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.002 0.000 HIS B 313 PHE 0.015 0.001 PHE A 610 TYR 0.014 0.002 TYR B 352 ARG 0.006 0.000 ARG B 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 138 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.699 Fit side-chains REVERT: A 377 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6428 (tp) REVERT: A 448 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7389 (ttp-110) REVERT: A 477 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8158 (mm) REVERT: A 499 HIS cc_start: 0.8275 (OUTLIER) cc_final: 0.7892 (m-70) REVERT: A 511 PHE cc_start: 0.9036 (t80) cc_final: 0.8810 (t80) REVERT: B 377 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6414 (tp) REVERT: B 439 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8367 (tt) REVERT: B 448 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7302 (ttm110) REVERT: B 477 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8166 (mm) REVERT: B 499 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.7897 (m-70) REVERT: B 511 PHE cc_start: 0.9037 (t80) cc_final: 0.8813 (t80) outliers start: 29 outliers final: 14 residues processed: 124 average time/residue: 0.7170 time to fit residues: 97.0716 Evaluate side-chains 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 2 optimal weight: 0.0010 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.182222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.146255 restraints weight = 8757.800| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.39 r_work: 0.3589 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6866 Z= 0.199 Angle : 0.565 6.144 9318 Z= 0.306 Chirality : 0.041 0.132 1006 Planarity : 0.004 0.033 1122 Dihedral : 8.894 54.964 960 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.75 % Allowed : 21.33 % 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: 1.24 (0.29), residues: 776 helix: 1.73 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.72 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 327 HIS 0.002 0.000 HIS B 313 PHE 0.015 0.002 PHE A 257 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 124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.657 Fit side-chains REVERT: A 261 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.7928 (t) REVERT: A 377 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6422 (tp) REVERT: A 448 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7348 (ttm110) REVERT: A 477 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8133 (mm) REVERT: B 261 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.7929 (t) REVERT: B 377 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6407 (tp) REVERT: B 439 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8349 (tt) REVERT: B 448 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7365 (ttm110) REVERT: B 477 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8148 (mm) outliers start: 26 outliers final: 12 residues processed: 114 average time/residue: 0.7190 time to fit residues: 89.1219 Evaluate side-chains 113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 448 ARG Chi-restraints excluded: chain A residue 477 LEU 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 477 LEU Chi-restraints excluded: chain B residue 552 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.180797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144708 restraints weight = 8666.386| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.38 r_work: 0.3582 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1941 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= 0.215 Angle : 0.576 6.090 9318 Z= 0.313 Chirality : 0.041 0.138 1006 Planarity : 0.004 0.034 1122 Dihedral : 8.621 52.101 960 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.31 % Allowed : 21.76 % 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: 1.72 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.72 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.001 0.001 HIS B 313 PHE 0.014 0.001 PHE A 391 TYR 0.013 0.002 TYR B 352 ARG 0.005 0.000 ARG B 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 122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.739 Fit side-chains REVERT: A 261 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.7916 (t) REVERT: A 377 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6428 (tp) REVERT: A 448 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7360 (ttm110) REVERT: A 477 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8116 (mm) REVERT: B 261 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.7919 (t) REVERT: B 377 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6417 (tp) REVERT: B 439 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8357 (tt) REVERT: B 448 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7393 (ttm110) REVERT: B 477 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8128 (mm) outliers start: 23 outliers final: 12 residues processed: 114 average time/residue: 0.7636 time to fit residues: 94.5896 Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 448 ARG Chi-restraints excluded: chain A residue 477 LEU 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 477 LEU 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 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.0010 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 = 0.180553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144511 restraints weight = 8825.729| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.37 r_work: 0.3579 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6866 Z= 0.233 Angle : 0.588 6.304 9318 Z= 0.320 Chirality : 0.042 0.156 1006 Planarity : 0.004 0.034 1122 Dihedral : 8.433 49.849 960 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.46 % Allowed : 22.33 % Favored : 74.21 % 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: 1.12 (0.29), residues: 776 helix: 1.62 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.69 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.002 0.001 HIS B 616 PHE 0.023 0.002 PHE A 391 TYR 0.014 0.002 TYR A 352 ARG 0.004 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 124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.723 Fit side-chains REVERT: A 261 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.7908 (t) REVERT: A 377 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6468 (tp) REVERT: A 448 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7377 (ttm110) REVERT: A 477 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8130 (mm) REVERT: A 590 ASP cc_start: 0.8174 (m-30) cc_final: 0.7960 (m-30) REVERT: B 261 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.7911 (t) REVERT: B 377 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6458 (tp) REVERT: B 439 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8370 (tt) REVERT: B 448 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7394 (ttm110) REVERT: B 477 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8138 (mm) REVERT: B 590 ASP cc_start: 0.8159 (m-30) cc_final: 0.7935 (m-30) outliers start: 24 outliers final: 12 residues processed: 116 average time/residue: 0.6637 time to fit residues: 84.2245 Evaluate side-chains 117 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 448 ARG Chi-restraints excluded: chain A residue 477 LEU 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 477 LEU 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: 6.9990 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 52 optimal weight: 0.0050 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.183722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.148100 restraints weight = 8729.293| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.37 r_work: 0.3617 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6866 Z= 0.190 Angle : 0.573 6.652 9318 Z= 0.311 Chirality : 0.041 0.136 1006 Planarity : 0.003 0.033 1122 Dihedral : 8.040 45.066 960 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.31 % Allowed : 23.05 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.29), residues: 776 helix: 1.73 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -1.73 (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 A 476 PHE 0.022 0.001 PHE A 391 TYR 0.014 0.001 TYR A 352 ARG 0.005 0.000 ARG B 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3882.84 seconds wall clock time: 69 minutes 33.48 seconds (4173.48 seconds total)