Starting phenix.real_space_refine on Tue Mar 11 23:24:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ijy_60645/03_2025/9ijy_60645_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ijy_60645/03_2025/9ijy_60645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ijy_60645/03_2025/9ijy_60645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ijy_60645/03_2025/9ijy_60645.map" model { file = "/net/cci-nas-00/data/ceres_data/9ijy_60645/03_2025/9ijy_60645_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ijy_60645/03_2025/9ijy_60645_trim.cif" } resolution = 2.64 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= 0.057 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 6 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: 5.91, per 1000 atoms: 0.89 Number of scatterers: 6654 At special positions: 0 Unit cell: (71.764, 123.956, 78.288, 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: 1.78 Conformation dependent library (CDL) restraints added in 873.2 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 76.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 230 through 257 Processing helix chain 'A' and resid 265 through 294 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: 3.923A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.807A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 removed outlier: 3.594A pdb=" N HIS A 441 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 442 " --> pdb=" O ILE A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 442' Processing helix chain 'A' and resid 446 through 470 removed outlier: 3.873A pdb=" N ILE A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 475 through 503 removed outlier: 4.170A pdb=" N GLU A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 532 removed outlier: 4.536A pdb=" N VAL A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 582 removed outlier: 4.012A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 618 Proline residue: A 598 - end of helix removed outlier: 3.823A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.734A 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 294 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: 3.923A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 403 through 419 removed outlier: 3.807A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 442 removed outlier: 3.594A pdb=" N HIS B 441 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS B 442 " --> pdb=" O ILE B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 442' Processing helix chain 'B' and resid 446 through 470 removed outlier: 3.873A pdb=" N ILE B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 475 through 503 removed outlier: 4.170A pdb=" N GLU B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 532 removed outlier: 4.536A pdb=" N VAL B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 582 removed outlier: 4.012A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 618 Proline residue: B 598 - end of helix removed outlier: 3.823A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1368 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: 1.84 Time building geometry restraints manager: 2.08 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: 950 1.31 - 1.43: 2110 1.43 - 1.56: 3758 1.56 - 1.68: 4 1.68 - 1.81: 44 Bond restraints: 6866 Sorted by residual: bond pdb=" CA ARG A 603 " pdb=" C ARG A 603 " ideal model delta sigma weight residual 1.523 1.446 0.077 1.30e-02 5.92e+03 3.54e+01 bond pdb=" CA ARG B 603 " pdb=" C ARG B 603 " ideal model delta sigma weight residual 1.523 1.446 0.077 1.30e-02 5.92e+03 3.54e+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=" 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=" C ARG A 603 " pdb=" O ARG A 603 " ideal model delta sigma weight residual 1.237 1.179 0.057 1.17e-02 7.31e+03 2.40e+01 ... (remaining 6861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 9244 3.79 - 7.57: 64 7.57 - 11.36: 6 11.36 - 15.14: 0 15.14 - 18.93: 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 119.71 100.78 18.93 3.00e+00 1.11e-01 3.98e+01 angle pdb=" O1P 6PL B1002 " pdb=" P 6PL B1002 " pdb=" O2P 6PL B1002 " ideal model delta sigma weight residual 119.71 100.78 18.93 3.00e+00 1.11e-01 3.98e+01 angle pdb=" O3P 6PL A1002 " pdb=" P 6PL A1002 " pdb=" O4P 6PL A1002 " ideal model delta sigma weight residual 93.65 110.81 -17.16 3.00e+00 1.11e-01 3.27e+01 angle pdb=" O3P 6PL B1002 " pdb=" P 6PL B1002 " pdb=" O4P 6PL B1002 " ideal model delta sigma weight residual 93.65 110.81 -17.16 3.00e+00 1.11e-01 3.27e+01 angle pdb=" O PHE A 602 " pdb=" C PHE A 602 " pdb=" N ARG A 603 " ideal model delta sigma weight residual 122.15 118.12 4.03 1.14e+00 7.69e-01 1.25e+01 ... (remaining 9313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 3316 16.33 - 32.65: 428 32.65 - 48.98: 134 48.98 - 65.30: 34 65.30 - 81.63: 8 Dihedral angle restraints: 3920 sinusoidal: 1610 harmonic: 2310 Sorted by residual: 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 -162.98 -17.02 0 5.00e+00 4.00e-02 1.16e+01 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 -162.98 -17.02 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CG ARG B 468 " pdb=" CD ARG B 468 " pdb=" NE ARG B 468 " pdb=" CZ ARG B 468 " ideal model delta sinusoidal sigma weight residual 90.00 132.85 -42.85 2 1.50e+01 4.44e-03 9.87e+00 ... (remaining 3917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 792 0.049 - 0.098: 192 0.098 - 0.147: 14 0.147 - 0.196: 6 0.196 - 0.245: 2 Chirality restraints: 1006 Sorted by residual: chirality pdb=" CA ARG B 603 " pdb=" N ARG B 603 " pdb=" C ARG B 603 " pdb=" CB ARG B 603 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ARG A 603 " pdb=" N ARG A 603 " pdb=" C ARG A 603 " pdb=" CB ARG A 603 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 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 0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 1003 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 549 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" CD GLU B 549 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU B 549 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU B 549 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 549 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" CD GLU A 549 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU A 549 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU A 549 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 475 " -0.005 2.00e-02 2.50e+03 1.04e-02 1.08e+00 pdb=" C PRO B 475 " 0.018 2.00e-02 2.50e+03 pdb=" O PRO B 475 " -0.007 2.00e-02 2.50e+03 pdb=" N HIS B 476 " -0.006 2.00e-02 2.50e+03 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 914 2.75 - 3.29: 6860 3.29 - 3.83: 11788 3.83 - 4.36: 13723 4.36 - 4.90: 23451 Nonbonded interactions: 56736 Sorted by model distance: nonbonded pdb=" O ILE A 271 " pdb=" OH TYR A 352 " model vdw 2.215 3.040 nonbonded pdb=" O ILE B 271 " pdb=" OH TYR B 352 " model vdw 2.215 3.040 nonbonded pdb=" O ASN B 618 " pdb=" OD1 ASN B 618 " model vdw 2.245 3.040 nonbonded pdb=" O ASN A 618 " pdb=" OD1 ASN A 618 " model vdw 2.245 3.040 nonbonded pdb=" O TRP B 534 " pdb=" NH1 ARG B 548 " model vdw 2.254 3.120 ... (remaining 56731 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.870 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:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 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 : 0.005 0.103 6866 Z= 0.362 Angle : 0.837 18.927 9318 Z= 0.411 Chirality : 0.042 0.245 1006 Planarity : 0.004 0.032 1122 Dihedral : 16.724 81.626 2426 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.29 % Allowed : 24.21 % 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: 0.06 (0.29), residues: 776 helix: 0.93 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -2.41 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 514 HIS 0.003 0.001 HIS B 476 PHE 0.012 0.001 PHE A 610 TYR 0.008 0.001 TYR A 512 ARG 0.006 0.001 ARG A 603 *********************** 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 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.794 Fit side-chains REVERT: A 532 MET cc_start: 0.8617 (mmm) cc_final: 0.8342 (mmp) REVERT: A 592 ILE cc_start: 0.8170 (pt) cc_final: 0.7675 (pt) REVERT: B 532 MET cc_start: 0.8617 (mmm) cc_final: 0.8342 (mmp) REVERT: B 592 ILE cc_start: 0.8168 (pt) cc_final: 0.7673 (pt) outliers start: 2 outliers final: 2 residues processed: 126 average time/residue: 1.0592 time to fit residues: 141.4436 Evaluate side-chains 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 570 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 6.9990 chunk 59 optimal weight: 0.0670 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 61 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 70 optimal weight: 0.0980 overall best weight: 0.2118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 618 ASN B 294 GLN B 618 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.179286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137040 restraints weight = 7706.246| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.24 r_work: 0.3475 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6866 Z= 0.171 Angle : 0.574 7.576 9318 Z= 0.298 Chirality : 0.040 0.142 1006 Planarity : 0.004 0.054 1122 Dihedral : 10.620 72.570 968 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.19 % Allowed : 19.88 % 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: 1.08 (0.29), residues: 776 helix: 1.71 (0.20), residues: 558 sheet: None (None), residues: 0 loop : -1.99 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 514 HIS 0.002 0.001 HIS B 441 PHE 0.019 0.001 PHE B 391 TYR 0.012 0.001 TYR A 352 ARG 0.005 0.000 ARG B 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 160 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.752 Fit side-chains REVERT: A 294 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.5961 (mp-120) REVERT: A 366 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.4487 (t80) REVERT: A 369 LYS cc_start: 0.7335 (pmtt) cc_final: 0.6971 (ptpp) REVERT: A 448 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.6483 (ptp90) REVERT: A 500 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8192 (mmmm) REVERT: A 570 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8117 (mmt180) REVERT: A 592 ILE cc_start: 0.8165 (pt) cc_final: 0.7698 (pt) REVERT: A 622 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7449 (mm-30) REVERT: B 294 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.5969 (mp-120) REVERT: B 366 PHE cc_start: 0.7129 (OUTLIER) cc_final: 0.4485 (t80) REVERT: B 369 LYS cc_start: 0.7333 (pmtt) cc_final: 0.6968 (ptpp) REVERT: B 448 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.6480 (ptp90) REVERT: B 500 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8192 (mmmm) REVERT: B 570 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8110 (mmt180) REVERT: B 592 ILE cc_start: 0.8158 (pt) cc_final: 0.7691 (pt) REVERT: B 622 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7454 (mm-30) outliers start: 36 outliers final: 8 residues processed: 142 average time/residue: 0.9832 time to fit residues: 148.2813 Evaluate side-chains 128 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 540 ASN A 608 ASN B 294 GLN B 540 ASN B 608 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.174065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130867 restraints weight = 7796.538| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.26 r_work: 0.3394 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6866 Z= 0.240 Angle : 0.603 7.364 9318 Z= 0.314 Chirality : 0.041 0.134 1006 Planarity : 0.004 0.042 1122 Dihedral : 10.532 69.879 968 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.34 % Allowed : 19.02 % 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: 1.14 (0.29), residues: 776 helix: 1.75 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -2.19 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 514 HIS 0.005 0.001 HIS B 616 PHE 0.021 0.002 PHE A 391 TYR 0.009 0.002 TYR B 272 ARG 0.004 0.000 ARG B 371 *********************** 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 148 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 0.772 Fit side-chains REVERT: A 253 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8629 (mm) REVERT: A 366 PHE cc_start: 0.6884 (OUTLIER) cc_final: 0.4566 (t80) REVERT: A 369 LYS cc_start: 0.7327 (pmtt) cc_final: 0.6986 (pttm) REVERT: A 511 PHE cc_start: 0.8931 (t80) cc_final: 0.8723 (t80) REVERT: A 550 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: A 584 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7376 (mt) REVERT: A 592 ILE cc_start: 0.8143 (pt) cc_final: 0.7729 (pt) REVERT: A 622 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7579 (mm-30) REVERT: B 253 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8635 (mm) REVERT: B 366 PHE cc_start: 0.6879 (OUTLIER) cc_final: 0.4562 (t80) REVERT: B 369 LYS cc_start: 0.7331 (pmtt) cc_final: 0.6989 (pttm) REVERT: B 511 PHE cc_start: 0.8931 (t80) cc_final: 0.8721 (t80) REVERT: B 550 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: B 584 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7370 (mt) REVERT: B 592 ILE cc_start: 0.8147 (pt) cc_final: 0.7731 (pt) REVERT: B 622 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7581 (mm-30) outliers start: 44 outliers final: 12 residues processed: 134 average time/residue: 1.1495 time to fit residues: 162.5885 Evaluate side-chains 118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 46 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 540 ASN A 618 ASN B 294 GLN B 540 ASN B 618 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.174032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130628 restraints weight = 7768.814| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.28 r_work: 0.3389 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6866 Z= 0.208 Angle : 0.578 7.434 9318 Z= 0.304 Chirality : 0.040 0.130 1006 Planarity : 0.004 0.037 1122 Dihedral : 10.175 64.814 968 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.76 % Allowed : 19.31 % 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: 1.25 (0.29), residues: 776 helix: 1.84 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -2.17 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 514 HIS 0.002 0.001 HIS A 441 PHE 0.017 0.002 PHE B 391 TYR 0.011 0.001 TYR A 352 ARG 0.003 0.000 ARG B 371 *********************** 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 152 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.681 Fit side-chains REVERT: A 366 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.4474 (t80) REVERT: A 369 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7024 (pttm) REVERT: A 550 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: A 584 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7386 (mt) REVERT: A 592 ILE cc_start: 0.8211 (pt) cc_final: 0.7836 (pt) REVERT: A 622 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: A 623 PHE cc_start: 0.6511 (m-80) cc_final: 0.6261 (m-10) REVERT: B 366 PHE cc_start: 0.6675 (OUTLIER) cc_final: 0.4470 (t80) REVERT: B 369 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7023 (pttm) REVERT: B 550 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7284 (mt-10) REVERT: B 584 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7385 (mt) REVERT: B 592 ILE cc_start: 0.8209 (pt) cc_final: 0.7834 (pt) REVERT: B 622 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7629 (mm-30) REVERT: B 623 PHE cc_start: 0.6518 (m-80) cc_final: 0.6265 (m-10) outliers start: 40 outliers final: 14 residues processed: 132 average time/residue: 1.1058 time to fit residues: 154.0415 Evaluate side-chains 132 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 21 optimal weight: 0.0170 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 540 ASN A 618 ASN B 294 GLN B 540 ASN B 618 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.174585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.131428 restraints weight = 7752.423| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.27 r_work: 0.3400 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6866 Z= 0.188 Angle : 0.573 7.569 9318 Z= 0.299 Chirality : 0.040 0.132 1006 Planarity : 0.004 0.035 1122 Dihedral : 9.809 60.894 968 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.19 % Allowed : 19.88 % 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: 1.39 (0.29), residues: 776 helix: 1.87 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -2.01 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 514 HIS 0.002 0.001 HIS B 441 PHE 0.014 0.002 PHE B 610 TYR 0.012 0.001 TYR B 352 ARG 0.003 0.000 ARG A 371 *********************** 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 150 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.745 Fit side-chains REVERT: A 366 PHE cc_start: 0.6628 (OUTLIER) cc_final: 0.4583 (t80) REVERT: A 369 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6947 (ptpp) REVERT: A 592 ILE cc_start: 0.8169 (pt) cc_final: 0.7835 (pt) REVERT: A 622 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7552 (mm-30) REVERT: B 366 PHE cc_start: 0.6619 (OUTLIER) cc_final: 0.4573 (t80) REVERT: B 369 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6942 (ptpp) REVERT: B 592 ILE cc_start: 0.8165 (pt) cc_final: 0.7831 (pt) REVERT: B 622 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7554 (mm-30) outliers start: 36 outliers final: 14 residues processed: 138 average time/residue: 1.0025 time to fit residues: 146.7478 Evaluate side-chains 130 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 0.0000 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 540 ASN A 618 ASN B 294 GLN B 540 ASN B 618 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.174597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131492 restraints weight = 7607.294| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.27 r_work: 0.3397 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6866 Z= 0.198 Angle : 0.597 9.301 9318 Z= 0.307 Chirality : 0.040 0.144 1006 Planarity : 0.004 0.033 1122 Dihedral : 9.613 57.556 968 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.32 % Allowed : 20.46 % 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: 1.37 (0.29), residues: 776 helix: 1.85 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -2.00 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 514 HIS 0.002 0.001 HIS A 476 PHE 0.014 0.002 PHE B 394 TYR 0.015 0.002 TYR B 272 ARG 0.003 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 140 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.814 Fit side-chains REVERT: A 366 PHE cc_start: 0.6533 (OUTLIER) cc_final: 0.4587 (t80) REVERT: A 369 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6903 (ptpp) REVERT: A 511 PHE cc_start: 0.8943 (t80) cc_final: 0.8719 (t80) REVERT: A 570 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8042 (mmt180) REVERT: A 592 ILE cc_start: 0.8165 (pt) cc_final: 0.7853 (pt) REVERT: A 622 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: B 366 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.4584 (t80) REVERT: B 369 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6897 (ptpp) REVERT: B 511 PHE cc_start: 0.8945 (t80) cc_final: 0.8718 (t80) REVERT: B 570 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8045 (mmt180) REVERT: B 592 ILE cc_start: 0.8162 (pt) cc_final: 0.7850 (pt) REVERT: B 622 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7369 (mm-30) outliers start: 30 outliers final: 10 residues processed: 126 average time/residue: 1.1318 time to fit residues: 150.6344 Evaluate side-chains 124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 608 ASN A 618 ASN B 294 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 608 ASN B 618 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.171741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.128407 restraints weight = 7725.579| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.26 r_work: 0.3361 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6866 Z= 0.259 Angle : 0.640 8.971 9318 Z= 0.328 Chirality : 0.042 0.162 1006 Planarity : 0.004 0.032 1122 Dihedral : 9.728 58.180 968 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: 1.19 (0.28), residues: 776 helix: 1.73 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -2.04 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 514 HIS 0.003 0.001 HIS B 476 PHE 0.016 0.002 PHE A 391 TYR 0.013 0.002 TYR B 272 ARG 0.004 0.000 ARG A 448 *********************** 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 144 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.680 Fit side-chains REVERT: A 366 PHE cc_start: 0.6466 (OUTLIER) cc_final: 0.4561 (t80) REVERT: A 369 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.6952 (ptpp) REVERT: A 495 LEU cc_start: 0.8755 (mp) cc_final: 0.8555 (mp) REVERT: A 550 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7266 (mt-10) REVERT: A 592 ILE cc_start: 0.8210 (pt) cc_final: 0.7907 (pt) REVERT: A 622 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7384 (mm-30) REVERT: A 623 PHE cc_start: 0.6632 (m-80) cc_final: 0.6280 (m-10) REVERT: B 366 PHE cc_start: 0.6460 (OUTLIER) cc_final: 0.4559 (t80) REVERT: B 369 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6948 (ptpp) REVERT: B 550 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: B 592 ILE cc_start: 0.8214 (pt) cc_final: 0.7911 (pt) REVERT: B 622 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7391 (mm-30) REVERT: B 623 PHE cc_start: 0.6638 (m-80) cc_final: 0.6283 (m-10) outliers start: 34 outliers final: 14 residues processed: 126 average time/residue: 1.1278 time to fit residues: 149.9597 Evaluate side-chains 128 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 622 GLU 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: 0.5980 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 19 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 618 ASN B 294 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 618 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.173582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.130356 restraints weight = 7817.189| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.27 r_work: 0.3383 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2348 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= 0.202 Angle : 0.621 9.942 9318 Z= 0.317 Chirality : 0.041 0.141 1006 Planarity : 0.004 0.033 1122 Dihedral : 9.569 56.954 968 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.03 % Allowed : 20.03 % Favored : 75.94 % 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: 1.28 (0.28), residues: 776 helix: 1.80 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -1.97 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 514 HIS 0.002 0.001 HIS B 476 PHE 0.017 0.002 PHE A 394 TYR 0.015 0.002 TYR B 496 ARG 0.004 0.000 ARG B 448 *********************** 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 136 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.695 Fit side-chains REVERT: A 366 PHE cc_start: 0.6190 (OUTLIER) cc_final: 0.4632 (t80) REVERT: A 369 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6930 (ptpp) REVERT: A 495 LEU cc_start: 0.8755 (mp) cc_final: 0.8542 (mp) REVERT: A 592 ILE cc_start: 0.8180 (pt) cc_final: 0.7881 (pt) REVERT: A 622 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7365 (mm-30) REVERT: B 366 PHE cc_start: 0.6183 (OUTLIER) cc_final: 0.4630 (t80) REVERT: B 369 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6927 (ptpp) REVERT: B 592 ILE cc_start: 0.8186 (pt) cc_final: 0.7887 (pt) REVERT: B 622 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7373 (mm-30) outliers start: 28 outliers final: 12 residues processed: 124 average time/residue: 1.1076 time to fit residues: 145.0263 Evaluate side-chains 121 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 622 GLU 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: 1.9990 chunk 43 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 0.0010 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 452 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 618 ASN B 294 GLN B 452 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 618 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.174099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131084 restraints weight = 7779.463| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.28 r_work: 0.3396 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6866 Z= 0.203 Angle : 0.643 14.052 9318 Z= 0.327 Chirality : 0.041 0.158 1006 Planarity : 0.004 0.032 1122 Dihedral : 9.045 59.686 960 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.03 % Allowed : 19.88 % 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: 1.31 (0.29), residues: 776 helix: 1.73 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -1.69 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 327 HIS 0.003 0.001 HIS A 499 PHE 0.014 0.002 PHE B 610 TYR 0.026 0.002 TYR B 496 ARG 0.003 0.000 ARG A 371 *********************** 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 139 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.694 Fit side-chains REVERT: A 366 PHE cc_start: 0.6257 (OUTLIER) cc_final: 0.4737 (t80) REVERT: A 369 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6975 (ptpp) REVERT: A 500 LYS cc_start: 0.7982 (mmmm) cc_final: 0.7760 (mmmm) REVERT: A 622 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7314 (mm-30) REVERT: A 623 PHE cc_start: 0.6524 (OUTLIER) cc_final: 0.6204 (m-10) REVERT: B 366 PHE cc_start: 0.6253 (OUTLIER) cc_final: 0.4740 (t80) REVERT: B 369 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6975 (ptpp) REVERT: B 500 LYS cc_start: 0.8037 (mmmm) cc_final: 0.7837 (mmmm) REVERT: B 622 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7321 (mm-30) REVERT: B 623 PHE cc_start: 0.6532 (OUTLIER) cc_final: 0.6211 (m-10) outliers start: 28 outliers final: 8 residues processed: 125 average time/residue: 1.0805 time to fit residues: 142.9390 Evaluate side-chains 120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 623 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.0030 chunk 75 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 618 ASN B 452 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 618 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.173775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130957 restraints weight = 7916.872| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.28 r_work: 0.3395 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6866 Z= 0.206 Angle : 0.657 15.105 9318 Z= 0.329 Chirality : 0.042 0.186 1006 Planarity : 0.004 0.032 1122 Dihedral : 8.965 59.252 960 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.74 % Allowed : 20.75 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.29), residues: 776 helix: 1.66 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -1.84 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 573 HIS 0.003 0.001 HIS A 499 PHE 0.014 0.002 PHE A 610 TYR 0.028 0.002 TYR A 496 ARG 0.004 0.000 ARG B 448 ********************** 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 127 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.686 Fit side-chains REVERT: A 310 ASN cc_start: 0.7606 (p0) cc_final: 0.7260 (p0) REVERT: A 366 PHE cc_start: 0.6163 (OUTLIER) cc_final: 0.4747 (t80) REVERT: A 369 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.7007 (ptpp) REVERT: A 622 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: A 623 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.6209 (m-10) REVERT: B 310 ASN cc_start: 0.7601 (p0) cc_final: 0.7257 (p0) REVERT: B 366 PHE cc_start: 0.6159 (OUTLIER) cc_final: 0.4751 (t80) REVERT: B 369 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.7003 (ptpp) REVERT: B 622 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: B 623 PHE cc_start: 0.6528 (OUTLIER) cc_final: 0.6216 (m-10) outliers start: 19 outliers final: 9 residues processed: 117 average time/residue: 1.0967 time to fit residues: 135.6969 Evaluate side-chains 124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 623 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 23 optimal weight: 0.0040 chunk 55 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 608 ASN A 618 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 608 ASN B 618 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.174130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131147 restraints weight = 7798.212| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.30 r_work: 0.3399 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6866 Z= 0.204 Angle : 0.664 14.608 9318 Z= 0.331 Chirality : 0.042 0.157 1006 Planarity : 0.004 0.032 1122 Dihedral : 8.968 59.193 960 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.03 % Allowed : 20.32 % Favored : 76.66 % 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: 1.15 (0.29), residues: 776 helix: 1.61 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.84 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 573 HIS 0.003 0.001 HIS B 499 PHE 0.014 0.002 PHE B 488 TYR 0.027 0.002 TYR A 496 ARG 0.004 0.000 ARG B 448 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4803.17 seconds wall clock time: 82 minutes 36.35 seconds (4956.35 seconds total)