Starting phenix.real_space_refine on Tue Feb 11 23:52:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ijy_60645/02_2025/9ijy_60645_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ijy_60645/02_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_60645/02_2025/9ijy_60645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ijy_60645/02_2025/9ijy_60645.map" model { file = "/net/cci-nas-00/data/ceres_data/9ijy_60645/02_2025/9ijy_60645_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ijy_60645/02_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-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: 5.58, per 1000 atoms: 0.84 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=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: 1.62 Conformation dependent library (CDL) restraints added in 858.1 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: 0.50 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: 1.79 Time building geometry restraints manager: 1.87 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: 3315 16.33 - 32.65: 426 32.65 - 48.98: 134 48.98 - 65.30: 34 65.30 - 81.63: 8 Dihedral angle restraints: 3917 sinusoidal: 1607 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 3914 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: 2.03 - 2.61: 77 2.61 - 3.18: 5942 3.18 - 3.75: 10973 3.75 - 4.33: 15050 4.33 - 4.90: 24697 Nonbonded interactions: 56739 Sorted by model distance: nonbonded pdb=" SG CYS B 415 " pdb=" SG CYS B 440 " model vdw 2.032 3.760 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 ... (remaining 56734 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: 1.640 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.090 Find NCS groups from input model: 0.100 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:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.290 ------------------------------------------------------------------------------- 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= 0.363 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 : 2.032 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 : 0.775 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: 1.0518 time to fit residues: 140.3073 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 : 0.815 ------------------------------------------------------------------------------- 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: 9.9990 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: 0.3180 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.177922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.135190 restraints weight = 7690.301| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.26 r_work: 0.3452 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6866 Z= 0.183 Angle : 0.578 7.631 9318 Z= 0.302 Chirality : 0.041 0.145 1006 Planarity : 0.004 0.057 1122 Dihedral : 10.627 71.196 968 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.48 % Allowed : 19.88 % 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: 1.05 (0.29), residues: 776 helix: 1.72 (0.20), residues: 552 sheet: None (None), residues: 0 loop : -2.00 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 514 HIS 0.005 0.001 HIS B 441 PHE 0.021 0.002 PHE A 391 TYR 0.011 0.001 TYR A 352 ARG 0.005 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 161 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.716 Fit side-chains REVERT: A 294 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6035 (mp-120) REVERT: A 366 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.4489 (t80) REVERT: A 369 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6936 (ptpp) REVERT: A 448 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6519 (ptp90) REVERT: A 500 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8183 (mmmm) REVERT: A 592 ILE cc_start: 0.8179 (pt) cc_final: 0.7717 (pt) REVERT: A 622 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: B 294 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6044 (mp-120) REVERT: B 366 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.4488 (t80) REVERT: B 369 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6934 (ptpp) REVERT: B 416 PHE cc_start: 0.6639 (t80) cc_final: 0.6395 (t80) REVERT: B 448 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6543 (ptp90) REVERT: B 500 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8185 (mmmm) REVERT: B 592 ILE cc_start: 0.8171 (pt) cc_final: 0.7709 (pt) REVERT: B 622 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7527 (mm-30) outliers start: 38 outliers final: 12 residues processed: 142 average time/residue: 1.0077 time to fit residues: 152.1825 Evaluate side-chains 129 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 448 ARG Chi-restraints excluded: chain A residue 477 LEU 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 369 LYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 477 LEU 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: 0.6980 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 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: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.173326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.129924 restraints weight = 7798.784| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.28 r_work: 0.3384 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6866 Z= 0.246 Angle : 0.606 7.642 9318 Z= 0.316 Chirality : 0.041 0.134 1006 Planarity : 0.004 0.042 1122 Dihedral : 10.532 69.625 968 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.91 % Allowed : 19.45 % 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: 1.08 (0.29), residues: 776 helix: 1.69 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -2.17 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 514 HIS 0.005 0.001 HIS B 616 PHE 0.020 0.002 PHE A 391 TYR 0.010 0.002 TYR A 290 ARG 0.004 0.000 ARG A 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 146 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 0.686 Fit side-chains REVERT: A 253 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8619 (mm) REVERT: A 366 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.4556 (t80) REVERT: A 369 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.7019 (pttm) REVERT: A 550 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7332 (mt-10) REVERT: A 584 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7377 (mt) REVERT: A 592 ILE cc_start: 0.8201 (pt) cc_final: 0.7788 (pt) REVERT: A 622 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7561 (mm-30) REVERT: A 623 PHE cc_start: 0.5981 (m-80) cc_final: 0.5687 (m-80) REVERT: B 253 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8620 (mm) REVERT: B 366 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.4552 (t80) REVERT: B 369 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7021 (pttm) REVERT: B 448 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6615 (ptp90) REVERT: B 550 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7337 (mt-10) REVERT: B 584 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7373 (mt) REVERT: B 592 ILE cc_start: 0.8201 (pt) cc_final: 0.7789 (pt) REVERT: B 622 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: B 623 PHE cc_start: 0.5984 (m-80) cc_final: 0.5690 (m-80) outliers start: 41 outliers final: 12 residues processed: 131 average time/residue: 1.1251 time to fit residues: 155.5532 Evaluate side-chains 124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 369 LYS 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 369 LYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 448 ARG 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: 0.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.0050 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.173176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.129427 restraints weight = 7766.518| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.28 r_work: 0.3377 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6866 Z= 0.226 Angle : 0.580 7.762 9318 Z= 0.304 Chirality : 0.041 0.131 1006 Planarity : 0.004 0.038 1122 Dihedral : 10.145 65.356 968 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.82 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: 1.19 (0.29), residues: 776 helix: 1.77 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -2.12 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 514 HIS 0.002 0.001 HIS A 616 PHE 0.017 0.002 PHE B 391 TYR 0.012 0.002 TYR A 352 ARG 0.003 0.000 ARG A 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 156 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 112 time to evaluate : 0.746 Fit side-chains REVERT: A 366 PHE cc_start: 0.6812 (OUTLIER) cc_final: 0.4506 (t80) REVERT: A 369 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.7012 (ptpp) REVERT: A 550 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: A 584 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7366 (mt) REVERT: A 592 ILE cc_start: 0.8233 (pt) cc_final: 0.7864 (pt) REVERT: A 622 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7653 (mm-30) REVERT: A 623 PHE cc_start: 0.6319 (m-80) cc_final: 0.6105 (m-10) REVERT: B 366 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.4504 (t80) REVERT: B 369 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.7011 (ptpp) REVERT: B 448 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6623 (ptp90) REVERT: B 550 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: B 584 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7365 (mt) REVERT: B 592 ILE cc_start: 0.8235 (pt) cc_final: 0.7866 (pt) REVERT: B 622 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: B 623 PHE cc_start: 0.6329 (m-80) cc_final: 0.6112 (m-10) outliers start: 44 outliers final: 14 residues processed: 134 average time/residue: 1.1276 time to fit residues: 159.3203 Evaluate side-chains 135 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 448 ARG 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: 0.5980 chunk 58 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 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 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 = 0.4062 r_free = 0.4062 target = 0.172798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129104 restraints weight = 7735.783| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.28 r_work: 0.3370 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6866 Z= 0.226 Angle : 0.594 7.992 9318 Z= 0.310 Chirality : 0.040 0.133 1006 Planarity : 0.004 0.036 1122 Dihedral : 9.910 63.009 968 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.04 % Allowed : 20.46 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.29), residues: 776 helix: 1.80 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -2.07 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 514 HIS 0.002 0.001 HIS B 476 PHE 0.017 0.002 PHE B 391 TYR 0.012 0.001 TYR A 352 ARG 0.003 0.000 ARG B 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: 35 poor density : 115 time to evaluate : 0.698 Fit side-chains REVERT: A 253 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8615 (mm) REVERT: A 366 PHE cc_start: 0.6681 (OUTLIER) cc_final: 0.4549 (t80) REVERT: A 369 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6958 (ptpp) REVERT: A 550 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: A 592 ILE cc_start: 0.8210 (pt) cc_final: 0.7869 (pt) REVERT: A 622 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7301 (mm-30) REVERT: A 623 PHE cc_start: 0.6319 (m-80) cc_final: 0.6101 (m-10) REVERT: B 253 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8621 (mm) REVERT: B 366 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.4544 (t80) REVERT: B 369 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6949 (ptpp) REVERT: B 550 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7292 (mt-10) REVERT: B 592 ILE cc_start: 0.8212 (pt) cc_final: 0.7871 (pt) REVERT: B 622 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7302 (mm-30) REVERT: B 623 PHE cc_start: 0.6330 (m-80) cc_final: 0.6108 (m-10) outliers start: 35 outliers final: 16 residues processed: 131 average time/residue: 1.1654 time to fit residues: 161.1107 Evaluate side-chains 132 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 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 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 253 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.172205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.128872 restraints weight = 7582.849| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.24 r_work: 0.3366 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2166 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= 0.234 Angle : 0.597 8.436 9318 Z= 0.312 Chirality : 0.041 0.137 1006 Planarity : 0.004 0.035 1122 Dihedral : 9.804 61.149 968 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.62 % Allowed : 19.45 % 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: 1.79 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -2.09 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 514 HIS 0.003 0.001 HIS A 616 PHE 0.014 0.002 PHE B 610 TYR 0.015 0.002 TYR A 496 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 151 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.733 Fit side-chains REVERT: A 366 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.4553 (t80) REVERT: A 369 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6956 (ptpp) REVERT: A 550 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: A 592 ILE cc_start: 0.8217 (pt) cc_final: 0.7900 (pt) REVERT: A 622 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7278 (mm-30) REVERT: A 623 PHE cc_start: 0.6321 (m-80) cc_final: 0.6091 (m-10) REVERT: B 366 PHE cc_start: 0.6606 (OUTLIER) cc_final: 0.4548 (t80) REVERT: B 369 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6947 (ptpp) REVERT: B 550 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: B 592 ILE cc_start: 0.8204 (pt) cc_final: 0.7887 (pt) REVERT: B 622 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: B 623 PHE cc_start: 0.6324 (m-80) cc_final: 0.6088 (m-10) outliers start: 39 outliers final: 16 residues processed: 128 average time/residue: 1.0993 time to fit residues: 148.7607 Evaluate side-chains 130 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 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 394 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 9 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 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 = 0.4057 r_free = 0.4057 target = 0.172261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.128898 restraints weight = 7677.537| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.25 r_work: 0.3367 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6866 Z= 0.223 Angle : 0.605 8.828 9318 Z= 0.316 Chirality : 0.041 0.140 1006 Planarity : 0.004 0.035 1122 Dihedral : 9.678 58.503 968 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.44 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: 1.29 (0.29), residues: 776 helix: 1.80 (0.20), residues: 568 sheet: None (None), residues: 0 loop : -1.90 (0.39), residues: 208 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 0.015 0.002 PHE B 610 TYR 0.027 0.002 TYR A 496 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 142 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.683 Fit side-chains REVERT: A 366 PHE cc_start: 0.6506 (OUTLIER) cc_final: 0.4520 (t80) REVERT: A 369 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6931 (ptpp) REVERT: A 570 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8146 (mmt180) REVERT: A 622 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7579 (mm-30) REVERT: A 623 PHE cc_start: 0.6380 (m-80) cc_final: 0.6098 (m-10) REVERT: B 366 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.4515 (t80) REVERT: B 369 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6929 (ptpp) REVERT: B 570 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8137 (mmt180) REVERT: B 592 ILE cc_start: 0.8211 (pt) cc_final: 0.7913 (pt) REVERT: B 622 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7360 (mm-30) REVERT: B 623 PHE cc_start: 0.6386 (m-80) cc_final: 0.6105 (m-10) outliers start: 30 outliers final: 10 residues processed: 130 average time/residue: 1.1208 time to fit residues: 153.9303 Evaluate side-chains 127 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 618 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 618 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.172605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128984 restraints weight = 7805.166| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.28 r_work: 0.3368 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6866 Z= 0.213 Angle : 0.607 9.130 9318 Z= 0.314 Chirality : 0.042 0.219 1006 Planarity : 0.004 0.035 1122 Dihedral : 9.579 55.844 968 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.76 % Allowed : 20.32 % 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: 1.34 (0.29), residues: 776 helix: 1.83 (0.20), residues: 568 sheet: None (None), residues: 0 loop : -1.85 (0.40), residues: 208 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 0.015 0.002 PHE A 610 TYR 0.019 0.001 TYR A 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 142 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.776 Fit side-chains REVERT: A 310 ASN cc_start: 0.7681 (p0) cc_final: 0.7388 (p0) REVERT: A 366 PHE cc_start: 0.6449 (OUTLIER) cc_final: 0.4582 (t80) REVERT: A 369 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.7031 (ptpp) REVERT: A 570 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8152 (mmt180) REVERT: A 622 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: A 623 PHE cc_start: 0.6342 (m-80) cc_final: 0.6066 (m-10) REVERT: B 310 ASN cc_start: 0.7677 (p0) cc_final: 0.7384 (p0) REVERT: B 366 PHE cc_start: 0.6442 (OUTLIER) cc_final: 0.4579 (t80) REVERT: B 369 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7025 (ptpp) REVERT: B 570 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8164 (mmt180) REVERT: B 622 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: B 623 PHE cc_start: 0.6357 (m-80) cc_final: 0.6077 (m-10) outliers start: 33 outliers final: 14 residues processed: 130 average time/residue: 1.1221 time to fit residues: 154.2076 Evaluate side-chains 129 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 570 ARG 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 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 500 LYS Chi-restraints excluded: chain B residue 570 ARG 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: 0.5980 chunk 43 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 59 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 452 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.173064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129749 restraints weight = 7723.055| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.27 r_work: 0.3377 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2366 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= 0.206 Angle : 0.615 9.451 9318 Z= 0.316 Chirality : 0.042 0.238 1006 Planarity : 0.004 0.034 1122 Dihedral : 9.505 57.686 968 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.89 % Allowed : 20.89 % 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: 1.30 (0.29), residues: 776 helix: 1.76 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.93 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 327 HIS 0.002 0.001 HIS A 616 PHE 0.014 0.002 PHE A 610 TYR 0.018 0.001 TYR A 496 ARG 0.004 0.000 ARG B 448 *********************** 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: 27 poor density : 112 time to evaluate : 0.690 Fit side-chains REVERT: A 366 PHE cc_start: 0.6181 (OUTLIER) cc_final: 0.4606 (t80) REVERT: A 369 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7018 (ptpp) REVERT: A 622 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: A 623 PHE cc_start: 0.6264 (m-80) cc_final: 0.6032 (m-10) REVERT: B 366 PHE cc_start: 0.6173 (OUTLIER) cc_final: 0.4605 (t80) REVERT: B 369 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.7013 (ptpp) REVERT: B 622 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7388 (mm-30) REVERT: B 623 PHE cc_start: 0.6285 (m-80) cc_final: 0.6045 (m-10) outliers start: 27 outliers final: 14 residues processed: 127 average time/residue: 1.1519 time to fit residues: 154.5641 Evaluate side-chains 129 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 500 LYS 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 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 500 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.1980 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 452 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 618 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 618 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.172371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129121 restraints weight = 7874.421| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.27 r_work: 0.3368 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6866 Z= 0.230 Angle : 0.642 9.791 9318 Z= 0.326 Chirality : 0.043 0.221 1006 Planarity : 0.004 0.033 1122 Dihedral : 9.081 58.641 960 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.46 % Allowed : 20.89 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.29), residues: 776 helix: 1.75 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -2.01 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 514 HIS 0.003 0.001 HIS A 616 PHE 0.015 0.002 PHE B 391 TYR 0.019 0.002 TYR A 496 ARG 0.004 0.001 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 130 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.765 Fit side-chains REVERT: A 366 PHE cc_start: 0.6235 (OUTLIER) cc_final: 0.4657 (t80) REVERT: A 369 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.7019 (ptpp) REVERT: A 622 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7382 (mm-30) REVERT: A 623 PHE cc_start: 0.6355 (m-80) cc_final: 0.6060 (m-10) REVERT: B 366 PHE cc_start: 0.6232 (OUTLIER) cc_final: 0.4658 (t80) REVERT: B 369 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7013 (ptpp) REVERT: B 622 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7691 (mm-30) REVERT: B 623 PHE cc_start: 0.6367 (m-80) cc_final: 0.6070 (m-10) outliers start: 24 outliers final: 14 residues processed: 116 average time/residue: 1.1244 time to fit residues: 137.9505 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 : 0.791 ------------------------------------------------------------------------------- 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 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 500 LYS 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 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 500 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 5.9990 chunk 23 optimal weight: 0.0010 chunk 55 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.173402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.130121 restraints weight = 7792.955| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.29 r_work: 0.3381 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6866 Z= 0.205 Angle : 0.628 9.882 9318 Z= 0.319 Chirality : 0.042 0.203 1006 Planarity : 0.004 0.032 1122 Dihedral : 9.027 59.612 960 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 : 2.88 % Allowed : 21.33 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.29), residues: 776 helix: 1.72 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.95 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 573 HIS 0.002 0.001 HIS B 499 PHE 0.014 0.002 PHE A 610 TYR 0.017 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: 4905.97 seconds wall clock time: 87 minutes 21.15 seconds (5241.15 seconds total)