Starting phenix.real_space_refine on Sat May 10 20:29:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ijy_60645/05_2025/9ijy_60645_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ijy_60645/05_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_60645/05_2025/9ijy_60645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ijy_60645/05_2025/9ijy_60645.map" model { file = "/net/cci-nas-00/data/ceres_data/9ijy_60645/05_2025/9ijy_60645_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ijy_60645/05_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-5687/modules/chem_data/mon_lib" Total number of atoms: 6654 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3270 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 13, 'TRANS': 378} Chain breaks: 1 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'6PL': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 6.11, per 1000 atoms: 0.92 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: 1.80 Conformation dependent library (CDL) restraints added in 926.6 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: 0.58 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: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.310 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 35.520 ------------------------------------------------------------------------------- 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 6868 Z= 0.292 Angle : 0.837 18.927 9322 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 Details of bonding type rmsd hydrogen bonds : bond 0.11180 ( 456) hydrogen bonds : angle 5.34194 ( 1368) SS BOND : bond 0.00094 ( 2) SS BOND : angle 0.08432 ( 4) covalent geometry : bond 0.00545 ( 6866) covalent geometry : angle 0.83710 ( 9318) *********************** 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 : 0.732 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: 0.9984 time to fit residues: 133.5745 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 : 0.784 ------------------------------------------------------------------------------- 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: 0.0470 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: 0.2078 ------------------------------------------------------------------------------- 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 = 0.179233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136943 restraints weight = 7705.479| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.24 r_work: 0.3473 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6868 Z= 0.133 Angle : 0.573 7.694 9322 Z= 0.298 Chirality : 0.040 0.140 1006 Planarity : 0.004 0.052 1122 Dihedral : 10.679 74.309 968 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.90 % Allowed : 19.88 % 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: 1.06 (0.29), residues: 776 helix: 1.69 (0.20), residues: 558 sheet: None (None), residues: 0 loop : -2.00 (0.39), 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 B 352 ARG 0.004 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.05175 ( 456) hydrogen bonds : angle 4.45003 ( 1368) SS BOND : bond 0.00003 ( 2) SS BOND : angle 0.03685 ( 4) covalent geometry : bond 0.00270 ( 6866) covalent geometry : angle 0.57322 ( 9318) *********************** 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 156 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.745 Fit side-chains REVERT: A 294 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.5915 (mp-120) REVERT: A 366 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.4503 (t80) REVERT: A 369 LYS cc_start: 0.7347 (pmtt) cc_final: 0.6993 (ptpp) REVERT: A 448 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.6488 (ptp90) REVERT: A 500 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8194 (mmmm) REVERT: A 592 ILE cc_start: 0.8168 (pt) cc_final: 0.7699 (pt) REVERT: B 294 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.5923 (mp-120) REVERT: B 366 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.4501 (t80) REVERT: B 369 LYS cc_start: 0.7342 (pmtt) cc_final: 0.6987 (ptpp) REVERT: B 448 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.6486 (ptp90) REVERT: B 500 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8193 (mmmm) REVERT: B 592 ILE cc_start: 0.8161 (pt) cc_final: 0.7691 (pt) outliers start: 34 outliers final: 10 residues processed: 140 average time/residue: 0.9005 time to fit residues: 134.5849 Evaluate side-chains 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4076 r_free = 0.4076 target = 0.174408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131151 restraints weight = 7798.722| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.28 r_work: 0.3398 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6868 Z= 0.166 Angle : 0.598 7.451 9322 Z= 0.312 Chirality : 0.041 0.134 1006 Planarity : 0.004 0.042 1122 Dihedral : 10.546 70.618 968 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.05 % Allowed : 19.88 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.29), residues: 776 helix: 1.74 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -2.23 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 514 HIS 0.003 0.001 HIS B 616 PHE 0.020 0.002 PHE A 391 TYR 0.009 0.002 TYR B 352 ARG 0.004 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.05230 ( 456) hydrogen bonds : angle 4.38805 ( 1368) SS BOND : bond 0.00029 ( 2) SS BOND : angle 0.07129 ( 4) covalent geometry : bond 0.00367 ( 6866) covalent geometry : angle 0.59812 ( 9318) *********************** 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: 42 poor density : 104 time to evaluate : 0.825 Fit side-chains REVERT: A 253 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8618 (mm) REVERT: A 304 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7259 (mt-10) REVERT: A 366 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.4622 (t80) REVERT: A 369 LYS cc_start: 0.7316 (pmtt) cc_final: 0.6969 (pttm) REVERT: A 550 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: A 584 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7353 (mt) REVERT: A 592 ILE cc_start: 0.8138 (pt) cc_final: 0.7719 (pt) REVERT: A 622 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7596 (mm-30) REVERT: B 253 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8633 (mm) REVERT: B 366 PHE cc_start: 0.6941 (OUTLIER) cc_final: 0.4618 (t80) REVERT: B 369 LYS cc_start: 0.7325 (pmtt) cc_final: 0.6975 (pttm) REVERT: B 550 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: B 584 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7351 (mt) REVERT: B 592 ILE cc_start: 0.8138 (pt) cc_final: 0.7718 (pt) REVERT: B 622 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7594 (mm-30) outliers start: 42 outliers final: 10 residues processed: 132 average time/residue: 1.0588 time to fit residues: 147.9083 Evaluate side-chains 118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 0.0770 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.175530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132524 restraints weight = 7774.714| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.28 r_work: 0.3412 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6868 Z= 0.141 Angle : 0.566 7.384 9322 Z= 0.297 Chirality : 0.040 0.130 1006 Planarity : 0.004 0.038 1122 Dihedral : 10.181 63.942 968 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.76 % Allowed : 19.60 % 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: 1.32 (0.29), residues: 776 helix: 1.84 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -2.10 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 514 HIS 0.002 0.001 HIS A 441 PHE 0.016 0.002 PHE A 391 TYR 0.011 0.001 TYR A 352 ARG 0.003 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.04903 ( 456) hydrogen bonds : angle 4.26694 ( 1368) SS BOND : bond 0.00003 ( 2) SS BOND : angle 0.07166 ( 4) covalent geometry : bond 0.00303 ( 6866) covalent geometry : angle 0.56566 ( 9318) *********************** 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 155 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 0.777 Fit side-chains REVERT: A 253 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8583 (mm) REVERT: A 366 PHE cc_start: 0.6717 (OUTLIER) cc_final: 0.4559 (t80) REVERT: A 369 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6906 (ptpp) REVERT: A 550 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: A 584 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7365 (mt) REVERT: A 592 ILE cc_start: 0.8184 (pt) cc_final: 0.7806 (pt) REVERT: A 622 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7676 (mm-30) REVERT: B 253 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8586 (mm) REVERT: B 366 PHE cc_start: 0.6712 (OUTLIER) cc_final: 0.4553 (t80) REVERT: B 369 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6908 (ptpp) REVERT: B 550 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: B 584 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7364 (mt) REVERT: B 592 ILE cc_start: 0.8186 (pt) cc_final: 0.7807 (pt) REVERT: B 622 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7675 (mm-30) outliers start: 40 outliers final: 12 residues processed: 135 average time/residue: 1.1035 time to fit residues: 157.3492 Evaluate side-chains 141 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 76 optimal weight: 0.0770 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.174371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.131064 restraints weight = 7758.743| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.29 r_work: 0.3395 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6868 Z= 0.147 Angle : 0.576 7.617 9322 Z= 0.301 Chirality : 0.040 0.132 1006 Planarity : 0.004 0.035 1122 Dihedral : 9.903 61.481 968 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.90 % Allowed : 20.75 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.29), residues: 776 helix: 1.93 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -2.07 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 514 HIS 0.002 0.001 HIS A 476 PHE 0.014 0.002 PHE A 391 TYR 0.011 0.001 TYR B 352 ARG 0.003 0.000 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.04940 ( 456) hydrogen bonds : angle 4.25659 ( 1368) SS BOND : bond 0.00026 ( 2) SS BOND : angle 0.10525 ( 4) covalent geometry : bond 0.00322 ( 6866) covalent geometry : angle 0.57621 ( 9318) *********************** 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 151 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.775 Fit side-chains REVERT: A 366 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.4584 (t80) REVERT: A 369 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6946 (ptpp) REVERT: A 592 ILE cc_start: 0.8164 (pt) cc_final: 0.7823 (pt) REVERT: A 622 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7686 (mm-30) REVERT: B 366 PHE cc_start: 0.6632 (OUTLIER) cc_final: 0.4576 (t80) REVERT: B 369 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6942 (ptpp) REVERT: B 592 ILE cc_start: 0.8163 (pt) cc_final: 0.7821 (pt) REVERT: B 622 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7577 (mm-30) outliers start: 34 outliers final: 16 residues processed: 137 average time/residue: 1.0088 time to fit residues: 146.4296 Evaluate side-chains 133 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 75 optimal weight: 0.9980 chunk 55 optimal weight: 0.0770 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 77 optimal weight: 0.0570 chunk 20 optimal weight: 3.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- 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 A 618 ASN B 294 GLN B 540 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 = 0.4094 r_free = 0.4094 target = 0.175598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.132521 restraints weight = 7638.202| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.27 r_work: 0.3410 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6868 Z= 0.135 Angle : 0.581 9.048 9322 Z= 0.299 Chirality : 0.039 0.135 1006 Planarity : 0.004 0.033 1122 Dihedral : 9.614 57.266 968 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: 1.48 (0.29), residues: 776 helix: 1.93 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -1.96 (0.39), residues: 200 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 0.016 0.002 PHE A 394 TYR 0.015 0.001 TYR A 272 ARG 0.003 0.000 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.04840 ( 456) hydrogen bonds : angle 4.20494 ( 1368) SS BOND : bond 0.00022 ( 2) SS BOND : angle 0.07998 ( 4) covalent geometry : bond 0.00289 ( 6866) covalent geometry : angle 0.58063 ( 9318) *********************** 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 148 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.801 Fit side-chains REVERT: A 366 PHE cc_start: 0.6524 (OUTLIER) cc_final: 0.4582 (t80) REVERT: A 369 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6917 (ptpp) REVERT: A 500 LYS cc_start: 0.7949 (mmmm) cc_final: 0.7538 (mmmm) REVERT: A 550 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7274 (mt-10) REVERT: A 570 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8009 (mmt180) REVERT: A 592 ILE cc_start: 0.8169 (pt) cc_final: 0.7851 (pt) REVERT: A 622 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: A 623 PHE cc_start: 0.6538 (OUTLIER) cc_final: 0.6186 (m-10) REVERT: B 366 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.4577 (t80) REVERT: B 369 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6919 (ptpp) REVERT: B 500 LYS cc_start: 0.7945 (mmmm) cc_final: 0.7536 (mmmm) REVERT: B 550 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7288 (mt-10) REVERT: B 592 ILE cc_start: 0.8162 (pt) cc_final: 0.7845 (pt) REVERT: B 622 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7371 (mm-30) REVERT: B 623 PHE cc_start: 0.6539 (OUTLIER) cc_final: 0.6187 (m-10) outliers start: 36 outliers final: 8 residues processed: 128 average time/residue: 1.1299 time to fit residues: 152.9770 Evaluate side-chains 128 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 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 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 550 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.0470 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 608 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 = 0.4089 r_free = 0.4089 target = 0.175211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.132202 restraints weight = 7725.539| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.28 r_work: 0.3407 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6868 Z= 0.139 Angle : 0.595 8.301 9322 Z= 0.308 Chirality : 0.040 0.167 1006 Planarity : 0.004 0.032 1122 Dihedral : 9.236 56.225 964 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.32 % Allowed : 20.17 % 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: 1.50 (0.29), residues: 776 helix: 1.94 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -1.95 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 327 HIS 0.002 0.001 HIS B 476 PHE 0.013 0.002 PHE B 610 TYR 0.017 0.002 TYR A 496 ARG 0.004 0.000 ARG B 448 Details of bonding type rmsd hydrogen bonds : bond 0.04823 ( 456) hydrogen bonds : angle 4.18997 ( 1368) SS BOND : bond 0.00011 ( 2) SS BOND : angle 0.04930 ( 4) covalent geometry : bond 0.00302 ( 6866) covalent geometry : angle 0.59496 ( 9318) *********************** 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 146 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.686 Fit side-chains REVERT: A 253 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8726 (mm) REVERT: A 366 PHE cc_start: 0.6198 (OUTLIER) cc_final: 0.4600 (t80) REVERT: A 369 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6914 (ptpp) REVERT: A 570 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8082 (mmt180) REVERT: A 592 ILE cc_start: 0.8163 (pt) cc_final: 0.7851 (pt) REVERT: A 622 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7312 (mm-30) REVERT: A 623 PHE cc_start: 0.6507 (OUTLIER) cc_final: 0.6159 (m-10) REVERT: B 253 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8735 (mm) REVERT: B 366 PHE cc_start: 0.6193 (OUTLIER) cc_final: 0.4599 (t80) REVERT: B 369 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6900 (ptpp) REVERT: B 550 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: B 592 ILE cc_start: 0.8151 (pt) cc_final: 0.7846 (pt) REVERT: B 622 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7590 (mm-30) REVERT: B 623 PHE cc_start: 0.6509 (OUTLIER) cc_final: 0.6158 (m-10) outliers start: 30 outliers final: 9 residues processed: 132 average time/residue: 1.0240 time to fit residues: 143.1683 Evaluate side-chains 138 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 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 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 A residue 623 PHE Chi-restraints excluded: chain B residue 253 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 477 LEU Chi-restraints excluded: chain B residue 550 GLU 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=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: 1.9990 chunk 1 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.174027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130994 restraints weight = 7839.006| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.29 r_work: 0.3390 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6868 Z= 0.151 Angle : 0.607 8.442 9322 Z= 0.313 Chirality : 0.041 0.157 1006 Planarity : 0.004 0.031 1122 Dihedral : 9.212 56.244 964 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.61 % Allowed : 20.32 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 776 helix: 1.88 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.94 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 327 HIS 0.002 0.001 HIS B 476 PHE 0.014 0.002 PHE B 391 TYR 0.035 0.002 TYR B 496 ARG 0.004 0.000 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.04939 ( 456) hydrogen bonds : angle 4.26739 ( 1368) SS BOND : bond 0.00032 ( 2) SS BOND : angle 0.05182 ( 4) covalent geometry : bond 0.00334 ( 6866) covalent geometry : angle 0.60689 ( 9318) *********************** 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 144 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.753 Fit side-chains REVERT: A 366 PHE cc_start: 0.6218 (OUTLIER) cc_final: 0.4666 (t80) REVERT: A 369 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.6935 (ptpp) REVERT: A 495 LEU cc_start: 0.8754 (mt) cc_final: 0.8529 (mp) REVERT: A 570 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8105 (mmt180) REVERT: A 592 ILE cc_start: 0.8170 (pt) cc_final: 0.7863 (pt) REVERT: A 622 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7342 (mm-30) REVERT: A 623 PHE cc_start: 0.6526 (OUTLIER) cc_final: 0.6177 (m-10) REVERT: B 366 PHE cc_start: 0.6213 (OUTLIER) cc_final: 0.4667 (t80) REVERT: B 369 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6931 (ptpp) REVERT: B 495 LEU cc_start: 0.8754 (mt) cc_final: 0.8530 (mp) REVERT: B 592 ILE cc_start: 0.8167 (pt) cc_final: 0.7860 (pt) REVERT: B 622 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7346 (mm-30) REVERT: B 623 PHE cc_start: 0.6527 (OUTLIER) cc_final: 0.6176 (m-10) outliers start: 32 outliers final: 12 residues processed: 127 average time/residue: 1.0532 time to fit residues: 141.4255 Evaluate side-chains 131 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 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 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 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 Chi-restraints excluded: chain B residue 623 PHE 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: 0.5980 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 618 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.172580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129482 restraints weight = 7830.679| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.27 r_work: 0.3376 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6868 Z= 0.163 Angle : 0.629 8.884 9322 Z= 0.322 Chirality : 0.042 0.241 1006 Planarity : 0.004 0.031 1122 Dihedral : 9.305 57.366 964 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.89 % Allowed : 20.32 % 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: 1.35 (0.29), residues: 776 helix: 1.85 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -1.97 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 327 HIS 0.003 0.001 HIS A 476 PHE 0.014 0.002 PHE B 391 TYR 0.028 0.002 TYR B 496 ARG 0.004 0.000 ARG B 448 Details of bonding type rmsd hydrogen bonds : bond 0.05064 ( 456) hydrogen bonds : angle 4.33821 ( 1368) SS BOND : bond 0.00008 ( 2) SS BOND : angle 0.04786 ( 4) covalent geometry : bond 0.00367 ( 6866) covalent geometry : angle 0.62871 ( 9318) *********************** 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 137 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.717 Fit side-chains REVERT: A 310 ASN cc_start: 0.7701 (p0) cc_final: 0.7408 (p0) REVERT: A 366 PHE cc_start: 0.6286 (OUTLIER) cc_final: 0.4773 (t80) REVERT: A 369 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6957 (ptpp) REVERT: A 495 LEU cc_start: 0.8760 (mt) cc_final: 0.8536 (mp) REVERT: A 570 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8151 (mmt180) REVERT: A 592 ILE cc_start: 0.8197 (pt) cc_final: 0.7902 (pt) REVERT: A 622 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7405 (mm-30) REVERT: B 310 ASN cc_start: 0.7588 (p0) cc_final: 0.7259 (p0) REVERT: B 366 PHE cc_start: 0.6281 (OUTLIER) cc_final: 0.4775 (t80) REVERT: B 369 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6952 (ptpp) REVERT: B 495 LEU cc_start: 0.8763 (mt) cc_final: 0.8540 (mp) REVERT: B 550 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: B 592 ILE cc_start: 0.8193 (pt) cc_final: 0.7897 (pt) REVERT: B 622 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7411 (mm-30) outliers start: 27 outliers final: 10 residues processed: 124 average time/residue: 1.0467 time to fit residues: 137.4318 Evaluate side-chains 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 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 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 550 GLU 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: 0.0670 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.174450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.131115 restraints weight = 7928.762| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.31 r_work: 0.3398 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6868 Z= 0.141 Angle : 0.616 9.197 9322 Z= 0.314 Chirality : 0.042 0.219 1006 Planarity : 0.004 0.031 1122 Dihedral : 9.233 59.920 964 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.17 % Allowed : 21.33 % 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: 1.43 (0.29), residues: 776 helix: 1.85 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.88 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 327 HIS 0.002 0.001 HIS A 476 PHE 0.014 0.002 PHE B 610 TYR 0.025 0.002 TYR A 496 ARG 0.004 0.000 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.04901 ( 456) hydrogen bonds : angle 4.31791 ( 1368) SS BOND : bond 0.00026 ( 2) SS BOND : angle 0.08932 ( 4) covalent geometry : bond 0.00310 ( 6866) covalent geometry : angle 0.61584 ( 9318) ********************** 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 133 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.789 Fit side-chains REVERT: A 366 PHE cc_start: 0.6172 (OUTLIER) cc_final: 0.4744 (t80) REVERT: A 369 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6949 (ptpp) REVERT: A 495 LEU cc_start: 0.8739 (mt) cc_final: 0.8494 (mp) REVERT: A 592 ILE cc_start: 0.8160 (pt) cc_final: 0.7859 (pt) REVERT: A 622 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7333 (mm-30) REVERT: B 366 PHE cc_start: 0.6167 (OUTLIER) cc_final: 0.4746 (t80) REVERT: B 369 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6921 (ptpp) REVERT: B 495 LEU cc_start: 0.8741 (mt) cc_final: 0.8498 (mp) REVERT: B 592 ILE cc_start: 0.8156 (pt) cc_final: 0.7854 (pt) REVERT: B 622 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7478 (mm-30) outliers start: 22 outliers final: 10 residues processed: 123 average time/residue: 1.0851 time to fit residues: 141.2195 Evaluate side-chains 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 chunk 55 optimal weight: 0.0980 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.174253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.131268 restraints weight = 7826.497| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.29 r_work: 0.3401 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6868 Z= 0.144 Angle : 0.621 9.137 9322 Z= 0.317 Chirality : 0.042 0.210 1006 Planarity : 0.004 0.031 1122 Dihedral : 8.993 59.716 960 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.03 % Allowed : 21.04 % 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: 1.41 (0.29), residues: 776 helix: 1.83 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.87 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 573 HIS 0.002 0.001 HIS A 616 PHE 0.014 0.002 PHE B 391 TYR 0.021 0.002 TYR A 496 ARG 0.006 0.001 ARG B 380 Details of bonding type rmsd hydrogen bonds : bond 0.04897 ( 456) hydrogen bonds : angle 4.31299 ( 1368) SS BOND : bond 0.00028 ( 2) SS BOND : angle 0.10951 ( 4) covalent geometry : bond 0.00318 ( 6866) covalent geometry : angle 0.62123 ( 9318) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4878.97 seconds wall clock time: 84 minutes 46.18 seconds (5086.18 seconds total)