Starting phenix.real_space_refine on Wed Sep 17 07:50:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ijy_60645/09_2025/9ijy_60645_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ijy_60645/09_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_60645/09_2025/9ijy_60645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ijy_60645/09_2025/9ijy_60645.map" model { file = "/net/cci-nas-00/data/ceres_data/9ijy_60645/09_2025/9ijy_60645_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ijy_60645/09_2025/9ijy_60645_trim.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.41, per 1000 atoms: 0.36 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: 0.58 Conformation dependent library (CDL) restraints added in 323.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.16 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: 1.00 Time building geometry restraints manager: 0.77 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: 0.01 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: 1.920 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.620 Find NCS groups from input model: 0.050 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:7.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.200 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG A 603 TYR 0.008 0.001 TYR A 512 PHE 0.012 0.001 PHE A 610 TRP 0.011 0.001 TRP B 514 HIS 0.003 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 6866) covalent geometry : angle 0.83710 ( 9318) SS BOND : bond 0.00094 ( 2) SS BOND : angle 0.08432 ( 4) hydrogen bonds : bond 0.11180 ( 456) hydrogen bonds : angle 5.34194 ( 1368) *********************** 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 : 0.204 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: 0.5270 time to fit residues: 70.0627 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 : 0.251 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4084 r_free = 0.4084 target = 0.175240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.131972 restraints weight = 7795.503| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.26 r_work: 0.3411 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1376 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= 0.157 Angle : 0.594 7.653 9322 Z= 0.312 Chirality : 0.042 0.147 1006 Planarity : 0.004 0.057 1122 Dihedral : 10.672 69.833 968 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.19 % Allowed : 19.88 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.29), residues: 776 helix: 1.66 (0.20), residues: 552 sheet: None (None), residues: 0 loop : -2.06 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 371 TYR 0.011 0.002 TYR B 352 PHE 0.021 0.002 PHE B 391 TRP 0.014 0.001 TRP B 514 HIS 0.003 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6866) covalent geometry : angle 0.59434 ( 9318) SS BOND : bond 0.00051 ( 2) SS BOND : angle 0.09004 ( 4) hydrogen bonds : bond 0.05263 ( 456) hydrogen bonds : angle 4.48158 ( 1368) *********************** 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 150 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.276 Fit side-chains REVERT: A 294 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6192 (mp-120) REVERT: A 304 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7255 (mt-10) REVERT: A 366 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.4447 (t80) REVERT: A 448 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6598 (ptp90) REVERT: A 500 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8173 (mmmm) REVERT: A 592 ILE cc_start: 0.8229 (pt) cc_final: 0.7781 (pt) REVERT: A 622 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7552 (mm-30) REVERT: B 294 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6203 (mp-120) REVERT: B 304 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7253 (mt-10) REVERT: B 366 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.4445 (t80) REVERT: B 448 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.6595 (ptp90) REVERT: B 500 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8175 (mmmm) REVERT: B 592 ILE cc_start: 0.8230 (pt) cc_final: 0.7781 (pt) REVERT: B 622 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7557 (mm-30) outliers start: 36 outliers final: 12 residues processed: 132 average time/residue: 0.5291 time to fit residues: 73.7785 Evaluate side-chains 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 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 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 36 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.0170 chunk 26 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 608 ASN B 618 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.175160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131895 restraints weight = 7684.732| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.27 r_work: 0.3406 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6868 Z= 0.146 Angle : 0.581 7.532 9322 Z= 0.303 Chirality : 0.041 0.143 1006 Planarity : 0.004 0.040 1122 Dihedral : 10.340 66.869 968 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.34 % Allowed : 19.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.29), residues: 776 helix: 1.72 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -2.22 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 371 TYR 0.010 0.001 TYR B 352 PHE 0.018 0.002 PHE B 391 TRP 0.012 0.001 TRP A 514 HIS 0.003 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6866) covalent geometry : angle 0.58138 ( 9318) SS BOND : bond 0.00019 ( 2) SS BOND : angle 0.09491 ( 4) hydrogen bonds : bond 0.05100 ( 456) hydrogen bonds : angle 4.36811 ( 1368) *********************** 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 156 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 112 time to evaluate : 0.240 Fit side-chains REVERT: A 253 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8605 (mm) REVERT: A 366 PHE cc_start: 0.6845 (OUTLIER) cc_final: 0.4549 (t80) REVERT: A 369 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6999 (pttm) REVERT: A 550 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: A 584 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7348 (mt) REVERT: A 592 ILE cc_start: 0.8173 (pt) cc_final: 0.7763 (pt) REVERT: A 622 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7577 (mm-30) REVERT: A 623 PHE cc_start: 0.5967 (m-80) cc_final: 0.5682 (m-80) REVERT: B 253 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8604 (mm) REVERT: B 366 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.4543 (t80) REVERT: B 369 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6998 (pttm) REVERT: B 550 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: B 584 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7348 (mt) REVERT: B 592 ILE cc_start: 0.8175 (pt) cc_final: 0.7766 (pt) REVERT: B 622 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7577 (mm-30) REVERT: B 623 PHE cc_start: 0.5969 (m-80) cc_final: 0.5682 (m-80) outliers start: 44 outliers final: 12 residues processed: 132 average time/residue: 0.5435 time to fit residues: 75.5229 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 : 0.266 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 0.0020 chunk 12 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.175301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131931 restraints weight = 7789.857| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.29 r_work: 0.3407 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6868 Z= 0.141 Angle : 0.571 7.320 9322 Z= 0.299 Chirality : 0.040 0.129 1006 Planarity : 0.004 0.036 1122 Dihedral : 10.037 62.744 968 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.29), residues: 776 helix: 1.85 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -2.13 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 371 TYR 0.010 0.001 TYR B 352 PHE 0.016 0.002 PHE A 391 TRP 0.011 0.001 TRP A 514 HIS 0.002 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6866) covalent geometry : angle 0.57143 ( 9318) SS BOND : bond 0.00022 ( 2) SS BOND : angle 0.11274 ( 4) hydrogen bonds : bond 0.04893 ( 456) hydrogen bonds : angle 4.29660 ( 1368) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.358 Fit side-chains REVERT: A 253 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8545 (mm) REVERT: A 366 PHE cc_start: 0.6716 (OUTLIER) cc_final: 0.4542 (t80) REVERT: A 369 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.7013 (pttm) REVERT: A 500 LYS cc_start: 0.8049 (mmmm) cc_final: 0.7849 (mmmm) REVERT: A 592 ILE cc_start: 0.8178 (pt) cc_final: 0.7807 (pt) REVERT: A 622 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7632 (mm-30) REVERT: B 253 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8550 (mm) REVERT: B 366 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.4534 (t80) REVERT: B 369 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.7014 (pttm) REVERT: B 592 ILE cc_start: 0.8177 (pt) cc_final: 0.7805 (pt) REVERT: B 622 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: B 623 PHE cc_start: 0.6268 (m-80) cc_final: 0.6062 (m-10) outliers start: 34 outliers final: 12 residues processed: 132 average time/residue: 0.5323 time to fit residues: 74.1216 Evaluate side-chains 132 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 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 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.171885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.128062 restraints weight = 7838.666| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.29 r_work: 0.3355 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6868 Z= 0.183 Angle : 0.613 7.588 9322 Z= 0.319 Chirality : 0.041 0.131 1006 Planarity : 0.004 0.035 1122 Dihedral : 9.995 63.584 968 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.90 % Allowed : 20.89 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.29), residues: 776 helix: 1.73 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -2.12 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 448 TYR 0.011 0.002 TYR B 352 PHE 0.018 0.002 PHE A 391 TRP 0.010 0.002 TRP A 514 HIS 0.004 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 6866) covalent geometry : angle 0.61333 ( 9318) SS BOND : bond 0.00023 ( 2) SS BOND : angle 0.05966 ( 4) hydrogen bonds : bond 0.05258 ( 456) hydrogen bonds : angle 4.38141 ( 1368) *********************** 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 145 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.267 Fit side-chains REVERT: A 366 PHE cc_start: 0.6649 (OUTLIER) cc_final: 0.4538 (t80) REVERT: A 550 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7263 (mt-10) REVERT: A 584 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7154 (mt) REVERT: A 592 ILE cc_start: 0.8213 (pt) cc_final: 0.7873 (pt) REVERT: A 622 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7390 (mm-30) REVERT: B 366 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.4536 (t80) REVERT: B 550 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7269 (mt-10) REVERT: B 584 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7143 (mt) REVERT: B 592 ILE cc_start: 0.8209 (pt) cc_final: 0.7872 (pt) REVERT: B 622 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7398 (mm-30) outliers start: 34 outliers final: 12 residues processed: 129 average time/residue: 0.5492 time to fit residues: 74.6025 Evaluate side-chains 124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 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 584 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 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 584 LEU 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 71 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.171134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.127149 restraints weight = 7846.026| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.27 r_work: 0.3338 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6868 Z= 0.188 Angle : 0.620 8.056 9322 Z= 0.325 Chirality : 0.042 0.140 1006 Planarity : 0.004 0.032 1122 Dihedral : 10.001 63.529 968 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.05 % Allowed : 18.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.29), residues: 776 helix: 1.69 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -2.14 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 448 TYR 0.020 0.002 TYR B 496 PHE 0.018 0.002 PHE A 391 TRP 0.009 0.002 TRP B 514 HIS 0.003 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 6866) covalent geometry : angle 0.61974 ( 9318) SS BOND : bond 0.00024 ( 2) SS BOND : angle 0.05336 ( 4) hydrogen bonds : bond 0.05315 ( 456) hydrogen bonds : angle 4.41702 ( 1368) *********************** 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: 42 poor density : 106 time to evaluate : 0.265 Fit side-chains REVERT: A 253 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8498 (mm) REVERT: A 366 PHE cc_start: 0.6548 (OUTLIER) cc_final: 0.4545 (t80) REVERT: A 550 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: A 592 ILE cc_start: 0.8235 (pt) cc_final: 0.7931 (pt) REVERT: A 622 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: B 253 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8501 (mm) REVERT: B 366 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.4547 (t80) REVERT: B 550 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: B 592 ILE cc_start: 0.8240 (pt) cc_final: 0.7935 (pt) REVERT: B 622 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7382 (mm-30) outliers start: 42 outliers final: 16 residues processed: 130 average time/residue: 0.5436 time to fit residues: 74.4761 Evaluate side-chains 128 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 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 582 THR 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 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 582 THR 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 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 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 294 GLN A 452 GLN A 540 ASN A 618 ASN B 294 GLN B 452 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 618 ASN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.171780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.128007 restraints weight = 7742.718| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.27 r_work: 0.3353 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6868 Z= 0.163 Angle : 0.614 8.523 9322 Z= 0.319 Chirality : 0.041 0.135 1006 Planarity : 0.004 0.033 1122 Dihedral : 9.829 61.330 968 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.62 % Allowed : 18.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.29), residues: 776 helix: 1.74 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -2.12 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 448 TYR 0.019 0.002 TYR A 496 PHE 0.016 0.002 PHE A 391 TRP 0.011 0.002 TRP A 514 HIS 0.003 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6866) covalent geometry : angle 0.61417 ( 9318) SS BOND : bond 0.00030 ( 2) SS BOND : angle 0.02701 ( 4) hydrogen bonds : bond 0.05127 ( 456) hydrogen bonds : angle 4.39722 ( 1368) *********************** 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 149 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.234 Fit side-chains REVERT: A 253 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8511 (mm) REVERT: A 366 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.4555 (t80) REVERT: A 369 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6783 (mttt) REVERT: A 550 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: A 570 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8155 (mmt180) REVERT: A 622 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7435 (mm-30) REVERT: B 253 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8513 (mm) REVERT: B 366 PHE cc_start: 0.6474 (OUTLIER) cc_final: 0.4554 (t80) REVERT: B 369 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6777 (mttt) REVERT: B 550 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: B 570 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8156 (mmt180) REVERT: B 622 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7429 (mm-30) outliers start: 39 outliers final: 15 residues processed: 128 average time/residue: 0.5573 time to fit residues: 75.1212 Evaluate side-chains 135 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 311 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 408 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 311 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 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 577 ILE Chi-restraints excluded: chain B residue 582 THR 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 11 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.170801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.127070 restraints weight = 7769.036| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.26 r_work: 0.3339 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6868 Z= 0.177 Angle : 0.622 8.961 9322 Z= 0.324 Chirality : 0.042 0.144 1006 Planarity : 0.004 0.033 1122 Dihedral : 9.802 60.184 968 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.33 % Allowed : 18.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.29), residues: 776 helix: 1.69 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -2.12 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 448 TYR 0.016 0.002 TYR A 496 PHE 0.017 0.002 PHE A 391 TRP 0.008 0.002 TRP B 514 HIS 0.003 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 6866) covalent geometry : angle 0.62179 ( 9318) SS BOND : bond 0.00011 ( 2) SS BOND : angle 0.05310 ( 4) hydrogen bonds : bond 0.05241 ( 456) hydrogen bonds : angle 4.42896 ( 1368) *********************** 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 140 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.202 Fit side-chains REVERT: A 253 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8460 (mm) REVERT: A 366 PHE cc_start: 0.6404 (OUTLIER) cc_final: 0.4532 (t80) REVERT: A 369 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.6799 (mttt) REVERT: A 622 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7353 (mm-30) REVERT: B 253 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8476 (mm) REVERT: B 366 PHE cc_start: 0.6399 (OUTLIER) cc_final: 0.4532 (t80) REVERT: B 369 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6783 (mttt) REVERT: B 500 LYS cc_start: 0.7964 (mmmm) cc_final: 0.7736 (mmmm) REVERT: B 622 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7356 (mm-30) outliers start: 37 outliers final: 12 residues processed: 125 average time/residue: 0.5263 time to fit residues: 69.3637 Evaluate side-chains 123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 311 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 408 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 311 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 408 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 570 ARG 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 13 optimal weight: 0.5980 chunk 61 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 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 540 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.171794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.128191 restraints weight = 7775.359| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.27 r_work: 0.3352 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6868 Z= 0.161 Angle : 0.624 9.519 9322 Z= 0.324 Chirality : 0.041 0.143 1006 Planarity : 0.004 0.034 1122 Dihedral : 9.666 57.012 968 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.46 % Allowed : 20.32 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.29), residues: 776 helix: 1.68 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -2.10 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 371 TYR 0.018 0.002 TYR A 496 PHE 0.015 0.002 PHE A 391 TRP 0.009 0.002 TRP A 327 HIS 0.002 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6866) covalent geometry : angle 0.62370 ( 9318) SS BOND : bond 0.00034 ( 2) SS BOND : angle 0.05282 ( 4) hydrogen bonds : bond 0.05068 ( 456) hydrogen bonds : angle 4.40791 ( 1368) *********************** 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 132 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.203 Fit side-chains REVERT: A 253 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8460 (mm) REVERT: A 366 PHE cc_start: 0.6106 (OUTLIER) cc_final: 0.4537 (t80) REVERT: A 369 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.6834 (mttt) REVERT: A 570 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8136 (mmt180) REVERT: A 622 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7388 (mm-30) REVERT: B 253 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8469 (mm) REVERT: B 366 PHE cc_start: 0.6103 (OUTLIER) cc_final: 0.4540 (t80) REVERT: B 369 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6831 (mttt) REVERT: B 570 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8142 (mmt180) REVERT: B 622 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7387 (mm-30) outliers start: 24 outliers final: 10 residues processed: 122 average time/residue: 0.5686 time to fit residues: 72.8454 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 : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 311 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 408 MET Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 311 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 408 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 570 ARG 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 53 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 chunk 62 optimal weight: 0.0030 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131250 restraints weight = 7788.973| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.26 r_work: 0.3394 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6868 Z= 0.135 Angle : 0.603 9.917 9322 Z= 0.311 Chirality : 0.041 0.152 1006 Planarity : 0.004 0.035 1122 Dihedral : 9.416 59.264 968 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.31 % Allowed : 21.33 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.29), residues: 776 helix: 1.80 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -2.00 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 380 TYR 0.016 0.001 TYR A 496 PHE 0.015 0.002 PHE B 391 TRP 0.011 0.002 TRP A 327 HIS 0.002 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6866) covalent geometry : angle 0.60288 ( 9318) SS BOND : bond 0.00008 ( 2) SS BOND : angle 0.03369 ( 4) hydrogen bonds : bond 0.04728 ( 456) hydrogen bonds : angle 4.31145 ( 1368) ********************** 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 129 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.314 Fit side-chains REVERT: A 253 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8455 (mm) REVERT: A 366 PHE cc_start: 0.6058 (OUTLIER) cc_final: 0.4643 (t80) REVERT: A 369 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.6789 (mttt) REVERT: B 253 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8459 (mm) REVERT: B 366 PHE cc_start: 0.6104 (OUTLIER) cc_final: 0.4543 (t80) REVERT: B 369 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6790 (mttt) outliers start: 23 outliers final: 5 residues processed: 119 average time/residue: 0.5123 time to fit residues: 64.4469 Evaluate side-chains 113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 577 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 77 optimal weight: 0.0020 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.173302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.129958 restraints weight = 7740.249| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.25 r_work: 0.3374 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6868 Z= 0.149 Angle : 0.621 10.019 9322 Z= 0.320 Chirality : 0.042 0.148 1006 Planarity : 0.004 0.034 1122 Dihedral : 8.970 57.198 960 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.31 % Allowed : 22.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.29), residues: 776 helix: 1.76 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -2.00 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 380 TYR 0.018 0.001 TYR A 496 PHE 0.014 0.002 PHE A 391 TRP 0.010 0.002 TRP A 573 HIS 0.002 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6866) covalent geometry : angle 0.62064 ( 9318) SS BOND : bond 0.00017 ( 2) SS BOND : angle 0.03160 ( 4) hydrogen bonds : bond 0.04866 ( 456) hydrogen bonds : angle 4.35112 ( 1368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2481.52 seconds wall clock time: 43 minutes 6.64 seconds (2586.64 seconds total)