Starting phenix.real_space_refine on Tue Feb 3 15:34:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ngo_49389/02_2026/9ngo_49389.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ngo_49389/02_2026/9ngo_49389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ngo_49389/02_2026/9ngo_49389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ngo_49389/02_2026/9ngo_49389.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ngo_49389/02_2026/9ngo_49389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ngo_49389/02_2026/9ngo_49389.map" } resolution = 3.01 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= 0.004 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 2771 2.51 5 N 735 2.21 5 O 803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4334 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1406 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain breaks: 5 Chain: "I" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1410 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain breaks: 1 Chain: "J" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 2 Time building chain proxies: 0.79, per 1000 atoms: 0.18 Number of scatterers: 4334 At special positions: 0 Unit cell: (107.25, 78.375, 91.575, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 803 8.00 N 735 7.00 C 2771 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.21 Conformation dependent library (CDL) restraints added in 119.1 milliseconds 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1040 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 4 sheets defined 52.7% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'H' and resid 496 through 498 No H-bonds generated for 'chain 'H' and resid 496 through 498' Processing helix chain 'H' and resid 499 through 504 removed outlier: 4.180A pdb=" N TYR H 503 " --> pdb=" O ASP H 499 " (cutoff:3.500A) Processing helix chain 'H' and resid 522 through 534 removed outlier: 3.780A pdb=" N LEU H 526 " --> pdb=" O PRO H 522 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS H 532 " --> pdb=" O TYR H 528 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU H 533 " --> pdb=" O GLN H 529 " (cutoff:3.500A) Processing helix chain 'H' and resid 570 through 590 Processing helix chain 'H' and resid 607 through 622 Processing helix chain 'H' and resid 664 through 681 Processing helix chain 'I' and resid 548 through 556 Processing helix chain 'I' and resid 567 through 583 removed outlier: 3.639A pdb=" N PHE I 581 " --> pdb=" O CYS I 577 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY I 583 " --> pdb=" O ARG I 579 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 617 Processing helix chain 'I' and resid 721 through 726 removed outlier: 4.101A pdb=" N GLN I 726 " --> pdb=" O SER I 722 " (cutoff:3.500A) Processing helix chain 'I' and resid 726 through 732 Processing helix chain 'I' and resid 765 through 777 removed outlier: 3.902A pdb=" N TYR I 769 " --> pdb=" O CYS I 765 " (cutoff:3.500A) Processing helix chain 'J' and resid 545 through 550 removed outlier: 4.161A pdb=" N LEU J 550 " --> pdb=" O SER J 547 " (cutoff:3.500A) Processing helix chain 'J' and resid 556 through 572 removed outlier: 3.543A pdb=" N ALA J 560 " --> pdb=" O ALA J 556 " (cutoff:3.500A) Processing helix chain 'J' and resid 572 through 579 removed outlier: 3.552A pdb=" N SER J 579 " --> pdb=" O ALA J 575 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 594 removed outlier: 4.138A pdb=" N THR J 594 " --> pdb=" O ALA J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 600 through 611 removed outlier: 4.178A pdb=" N VAL J 604 " --> pdb=" O LEU J 600 " (cutoff:3.500A) Processing helix chain 'J' and resid 615 through 634 removed outlier: 3.586A pdb=" N ALA J 619 " --> pdb=" O ARG J 615 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA J 633 " --> pdb=" O ALA J 629 " (cutoff:3.500A) Processing helix chain 'J' and resid 635 through 637 No H-bonds generated for 'chain 'J' and resid 635 through 637' Processing helix chain 'J' and resid 639 through 656 Processing helix chain 'J' and resid 662 through 670 removed outlier: 3.512A pdb=" N LYS J 666 " --> pdb=" O GLY J 662 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL J 668 " --> pdb=" O PHE J 664 " (cutoff:3.500A) Processing helix chain 'J' and resid 675 through 686 Processing helix chain 'J' and resid 691 through 706 removed outlier: 3.955A pdb=" N GLY J 695 " --> pdb=" O ARG J 691 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE J 703 " --> pdb=" O LEU J 699 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE J 704 " --> pdb=" O ARG J 700 " (cutoff:3.500A) Processing helix chain 'J' and resid 709 through 719 removed outlier: 3.587A pdb=" N TYR J 713 " --> pdb=" O ARG J 709 " (cutoff:3.500A) Processing helix chain 'J' and resid 732 through 737 Processing sheet with id=AA1, first strand: chain 'I' and resid 606 through 610 removed outlier: 4.752A pdb=" N LYS H 462 " --> pdb=" O LEU I 610 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR H 492 " --> pdb=" O LEU H 463 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 480 through 481 removed outlier: 3.607A pdb=" N VAL H 481 " --> pdb=" O GLY I 633 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY I 633 " --> pdb=" O VAL H 481 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 537 through 542 removed outlier: 3.666A pdb=" N GLY I 762 " --> pdb=" O THR H 514 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 561 through 562 removed outlier: 6.324A pdb=" N LEU I 561 " --> pdb=" O TYR I 589 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 232 hydrogen bonds defined for protein. 657 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: 0.63 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1406 1.34 - 1.46: 865 1.46 - 1.58: 2087 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 4397 Sorted by residual: bond pdb=" N GLU H 544 " pdb=" CA GLU H 544 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.87e+00 bond pdb=" C PRO I 704 " pdb=" N PRO I 705 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.89e+00 bond pdb=" CA GLU H 544 " pdb=" C GLU H 544 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.34e-02 5.57e+03 2.74e+00 bond pdb=" CG GLU J 626 " pdb=" CD GLU J 626 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.22e+00 bond pdb=" CB GLN H 529 " pdb=" CG GLN H 529 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.10e+00 ... (remaining 4392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 5636 2.08 - 4.16: 241 4.16 - 6.24: 41 6.24 - 8.32: 12 8.32 - 10.41: 2 Bond angle restraints: 5932 Sorted by residual: angle pdb=" C HIS I 711 " pdb=" CA HIS I 711 " pdb=" CB HIS I 711 " ideal model delta sigma weight residual 116.54 110.14 6.40 1.15e+00 7.56e-01 3.10e+01 angle pdb=" C LYS H 545 " pdb=" N PRO H 546 " pdb=" CA PRO H 546 " ideal model delta sigma weight residual 119.85 124.93 -5.08 1.01e+00 9.80e-01 2.53e+01 angle pdb=" CB LYS I 624 " pdb=" CG LYS I 624 " pdb=" CD LYS I 624 " ideal model delta sigma weight residual 111.30 121.22 -9.92 2.30e+00 1.89e-01 1.86e+01 angle pdb=" CA HIS I 711 " pdb=" C HIS I 711 " pdb=" N GLN I 712 " ideal model delta sigma weight residual 119.52 116.39 3.13 7.90e-01 1.60e+00 1.57e+01 angle pdb=" CA PRO H 560 " pdb=" N PRO H 560 " pdb=" CD PRO H 560 " ideal model delta sigma weight residual 112.00 106.63 5.37 1.40e+00 5.10e-01 1.47e+01 ... (remaining 5927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 2397 16.40 - 32.79: 248 32.79 - 49.19: 43 49.19 - 65.59: 13 65.59 - 81.99: 5 Dihedral angle restraints: 2706 sinusoidal: 1111 harmonic: 1595 Sorted by residual: dihedral pdb=" CA GLU I 627 " pdb=" C GLU I 627 " pdb=" N LEU I 628 " pdb=" CA LEU I 628 " ideal model delta harmonic sigma weight residual 180.00 -153.32 -26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" N GLU H 544 " pdb=" C GLU H 544 " pdb=" CA GLU H 544 " pdb=" CB GLU H 544 " ideal model delta harmonic sigma weight residual 122.80 133.46 -10.66 0 2.50e+00 1.60e-01 1.82e+01 dihedral pdb=" C GLU H 544 " pdb=" N GLU H 544 " pdb=" CA GLU H 544 " pdb=" CB GLU H 544 " ideal model delta harmonic sigma weight residual -122.60 -132.72 10.12 0 2.50e+00 1.60e-01 1.64e+01 ... (remaining 2703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 591 0.075 - 0.150: 93 0.150 - 0.225: 10 0.225 - 0.299: 1 0.299 - 0.374: 1 Chirality restraints: 696 Sorted by residual: chirality pdb=" CA GLU H 544 " pdb=" N GLU H 544 " pdb=" C GLU H 544 " pdb=" CB GLU H 544 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CB VAL I 564 " pdb=" CA VAL I 564 " pdb=" CG1 VAL I 564 " pdb=" CG2 VAL I 564 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU J 570 " pdb=" CB LEU J 570 " pdb=" CD1 LEU J 570 " pdb=" CD2 LEU J 570 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 693 not shown) Planarity restraints: 750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 559 " -0.054 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO H 560 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO H 560 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 560 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 557 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO I 558 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO I 558 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 558 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 551 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO J 552 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO J 552 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 552 " 0.027 5.00e-02 4.00e+02 ... (remaining 747 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 2484 3.04 - 3.51: 4705 3.51 - 3.97: 6492 3.97 - 4.44: 7469 4.44 - 4.90: 11814 Nonbonded interactions: 32964 Sorted by model distance: nonbonded pdb=" O TRP J 622 " pdb=" OE1 GLU J 626 " model vdw 2.575 3.040 nonbonded pdb=" N GLU H 559 " pdb=" O GLU H 559 " model vdw 2.605 2.496 nonbonded pdb=" O CYS I 744 " pdb=" OD1 ASN I 745 " model vdw 2.618 3.040 nonbonded pdb=" N SER I 713 " pdb=" O SER I 713 " model vdw 2.628 2.496 nonbonded pdb=" N ASN H 570 " pdb=" O ASN H 570 " model vdw 2.629 2.496 ... (remaining 32959 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.420 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.560 Find NCS groups from input model: 0.030 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5557 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 0.066 4397 Z= 0.212 Angle : 1.006 10.405 5932 Z= 0.533 Chirality : 0.055 0.374 696 Planarity : 0.006 0.080 750 Dihedral : 14.412 81.985 1666 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.21 % Allowed : 0.42 % Favored : 99.38 % Cbeta Deviations : 0.19 % 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 are not related in a simple way. whole: -1.03 (0.36), residues: 524 helix: -0.29 (0.32), residues: 241 sheet: -0.01 (0.57), residues: 71 loop : -1.27 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 709 TYR 0.016 0.002 TYR H 503 PHE 0.030 0.002 PHE H 551 TRP 0.029 0.004 TRP H 567 HIS 0.004 0.001 HIS H 493 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 4397) covalent geometry : angle 1.00590 ( 5932) hydrogen bonds : bond 0.14066 ( 232) hydrogen bonds : angle 6.41997 ( 657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 665 LEU cc_start: 0.5289 (mt) cc_final: 0.5041 (pp) REVERT: J 639 LEU cc_start: 0.7866 (mt) cc_final: 0.7649 (tp) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.0631 time to fit residues: 13.8509 Evaluate side-chains 111 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.0030 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 588 GLN I 607 GLN J 557 GLN ** J 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.150543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.136828 restraints weight = 14681.212| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 3.71 r_work: 0.4324 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4397 Z= 0.147 Angle : 0.778 12.473 5932 Z= 0.386 Chirality : 0.046 0.157 696 Planarity : 0.005 0.060 750 Dihedral : 5.047 21.566 586 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.50 % Allowed : 17.50 % Favored : 80.00 % 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 are not related in a simple way. whole: -0.61 (0.36), residues: 524 helix: 0.32 (0.33), residues: 242 sheet: 0.59 (0.62), residues: 65 loop : -1.53 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 709 TYR 0.020 0.003 TYR I 606 PHE 0.013 0.001 PHE J 620 TRP 0.014 0.002 TRP H 567 HIS 0.003 0.001 HIS J 715 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4397) covalent geometry : angle 0.77812 ( 5932) hydrogen bonds : bond 0.04067 ( 232) hydrogen bonds : angle 5.28467 ( 657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 479 GLN cc_start: 0.3511 (mp10) cc_final: 0.3218 (mp10) REVERT: H 665 LEU cc_start: 0.5737 (mt) cc_final: 0.5326 (pp) REVERT: I 594 HIS cc_start: 0.3024 (m90) cc_final: 0.1875 (m90) REVERT: J 620 PHE cc_start: 0.6202 (m-80) cc_final: 0.5913 (m-10) outliers start: 12 outliers final: 8 residues processed: 130 average time/residue: 0.0778 time to fit residues: 12.3822 Evaluate side-chains 110 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain I residue 547 ASP Chi-restraints excluded: chain I residue 597 VAL Chi-restraints excluded: chain I residue 603 THR Chi-restraints excluded: chain I residue 699 THR Chi-restraints excluded: chain J residue 544 PHE Chi-restraints excluded: chain J residue 554 THR Chi-restraints excluded: chain J residue 692 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 654 GLN ** J 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 715 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.147680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.133951 restraints weight = 14134.529| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 3.61 r_work: 0.4278 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4397 Z= 0.149 Angle : 0.735 12.161 5932 Z= 0.367 Chirality : 0.045 0.160 696 Planarity : 0.005 0.058 750 Dihedral : 4.790 20.601 586 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.96 % Allowed : 18.96 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.37), residues: 524 helix: 0.72 (0.33), residues: 242 sheet: 1.28 (0.64), residues: 60 loop : -1.32 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 675 TYR 0.019 0.002 TYR I 606 PHE 0.022 0.002 PHE J 735 TRP 0.012 0.002 TRP H 567 HIS 0.003 0.001 HIS J 715 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4397) covalent geometry : angle 0.73501 ( 5932) hydrogen bonds : bond 0.03816 ( 232) hydrogen bonds : angle 5.16162 ( 657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 665 LEU cc_start: 0.6115 (mt) cc_final: 0.5745 (pp) REVERT: I 594 HIS cc_start: 0.3716 (m90) cc_final: 0.1690 (m90) REVERT: J 655 GLU cc_start: 0.7185 (pt0) cc_final: 0.6960 (pt0) REVERT: J 670 GLU cc_start: 0.6273 (mt-10) cc_final: 0.5322 (mm-30) outliers start: 19 outliers final: 11 residues processed: 136 average time/residue: 0.0560 time to fit residues: 9.8916 Evaluate side-chains 123 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 608 HIS Chi-restraints excluded: chain H residue 636 SER Chi-restraints excluded: chain I residue 603 THR Chi-restraints excluded: chain I residue 637 MET Chi-restraints excluded: chain I residue 699 THR Chi-restraints excluded: chain I residue 713 SER Chi-restraints excluded: chain J residue 554 THR Chi-restraints excluded: chain J residue 692 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 515 GLN H 553 ASN ** I 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.146983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.132368 restraints weight = 14337.797| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 3.71 r_work: 0.4249 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4397 Z= 0.142 Angle : 0.714 8.203 5932 Z= 0.359 Chirality : 0.046 0.161 696 Planarity : 0.005 0.063 750 Dihedral : 4.790 20.009 586 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.92 % Allowed : 21.04 % Favored : 76.04 % 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 are not related in a simple way. whole: 0.15 (0.37), residues: 524 helix: 0.84 (0.33), residues: 243 sheet: 1.38 (0.62), residues: 60 loop : -1.09 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 738 TYR 0.017 0.002 TYR I 606 PHE 0.014 0.001 PHE J 620 TRP 0.008 0.001 TRP H 567 HIS 0.002 0.001 HIS I 594 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4397) covalent geometry : angle 0.71352 ( 5932) hydrogen bonds : bond 0.03577 ( 232) hydrogen bonds : angle 5.08062 ( 657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 665 LEU cc_start: 0.6410 (mt) cc_final: 0.5952 (pp) REVERT: I 594 HIS cc_start: 0.4166 (m90) cc_final: 0.1879 (m90) REVERT: J 670 GLU cc_start: 0.6373 (mt-10) cc_final: 0.5435 (mm-30) REVERT: J 737 LYS cc_start: 0.7018 (mmmt) cc_final: 0.6420 (mmmt) outliers start: 14 outliers final: 12 residues processed: 135 average time/residue: 0.0729 time to fit residues: 12.2837 Evaluate side-chains 121 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 608 HIS Chi-restraints excluded: chain H residue 636 SER Chi-restraints excluded: chain I residue 574 LEU Chi-restraints excluded: chain I residue 603 THR Chi-restraints excluded: chain I residue 699 THR Chi-restraints excluded: chain J residue 554 THR Chi-restraints excluded: chain J residue 571 ARG Chi-restraints excluded: chain J residue 604 VAL Chi-restraints excluded: chain J residue 692 THR Chi-restraints excluded: chain J residue 714 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 41 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 717 ASN ** J 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.146398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.132152 restraints weight = 14380.513| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 3.62 r_work: 0.4245 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4397 Z= 0.137 Angle : 0.768 22.518 5932 Z= 0.370 Chirality : 0.046 0.191 696 Planarity : 0.005 0.055 750 Dihedral : 4.687 20.435 586 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.17 % Allowed : 22.92 % Favored : 72.92 % 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 are not related in a simple way. whole: 0.23 (0.37), residues: 524 helix: 1.01 (0.33), residues: 243 sheet: 1.37 (0.62), residues: 60 loop : -1.17 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 709 TYR 0.017 0.002 TYR J 713 PHE 0.029 0.002 PHE I 581 TRP 0.010 0.001 TRP H 567 HIS 0.002 0.000 HIS I 565 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4397) covalent geometry : angle 0.76809 ( 5932) hydrogen bonds : bond 0.03605 ( 232) hydrogen bonds : angle 5.03585 ( 657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 607 MET cc_start: 0.5609 (mmm) cc_final: 0.5080 (mmm) REVERT: H 665 LEU cc_start: 0.6397 (mt) cc_final: 0.5970 (pp) REVERT: J 642 TYR cc_start: 0.6541 (t80) cc_final: 0.6010 (t80) outliers start: 20 outliers final: 15 residues processed: 128 average time/residue: 0.0561 time to fit residues: 9.1470 Evaluate side-chains 122 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 608 HIS Chi-restraints excluded: chain H residue 636 SER Chi-restraints excluded: chain I residue 574 LEU Chi-restraints excluded: chain I residue 603 THR Chi-restraints excluded: chain I residue 605 ILE Chi-restraints excluded: chain I residue 637 MET Chi-restraints excluded: chain I residue 699 THR Chi-restraints excluded: chain I residue 743 VAL Chi-restraints excluded: chain J residue 554 THR Chi-restraints excluded: chain J residue 571 ARG Chi-restraints excluded: chain J residue 604 VAL Chi-restraints excluded: chain J residue 714 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 12 optimal weight: 0.1980 chunk 20 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 747 GLN J 595 GLN ** J 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.145757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.133963 restraints weight = 14543.031| |-----------------------------------------------------------------------------| r_work (start): 0.4394 rms_B_bonded: 3.80 r_work: 0.4252 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.6694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4397 Z= 0.134 Angle : 0.764 19.335 5932 Z= 0.373 Chirality : 0.045 0.161 696 Planarity : 0.005 0.067 750 Dihedral : 4.599 19.599 586 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.17 % Allowed : 24.17 % Favored : 71.67 % 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 are not related in a simple way. whole: 0.27 (0.37), residues: 524 helix: 1.09 (0.33), residues: 243 sheet: 1.35 (0.62), residues: 60 loop : -1.20 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 720 TYR 0.017 0.002 TYR J 713 PHE 0.030 0.002 PHE I 581 TRP 0.012 0.002 TRP J 622 HIS 0.001 0.000 HIS I 604 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4397) covalent geometry : angle 0.76396 ( 5932) hydrogen bonds : bond 0.03515 ( 232) hydrogen bonds : angle 4.94097 ( 657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 558 GLN cc_start: 0.7630 (tt0) cc_final: 0.7377 (pt0) REVERT: H 665 LEU cc_start: 0.6679 (mt) cc_final: 0.6164 (pp) outliers start: 20 outliers final: 16 residues processed: 126 average time/residue: 0.0749 time to fit residues: 11.7980 Evaluate side-chains 125 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 608 HIS Chi-restraints excluded: chain H residue 636 SER Chi-restraints excluded: chain I residue 574 LEU Chi-restraints excluded: chain I residue 603 THR Chi-restraints excluded: chain I residue 605 ILE Chi-restraints excluded: chain I residue 637 MET Chi-restraints excluded: chain I residue 699 THR Chi-restraints excluded: chain I residue 743 VAL Chi-restraints excluded: chain I residue 744 CYS Chi-restraints excluded: chain J residue 554 THR Chi-restraints excluded: chain J residue 604 VAL Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 627 TYR Chi-restraints excluded: chain J residue 714 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 12 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 595 GLN ** J 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.144401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.131831 restraints weight = 14432.651| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 4.04 r_work: 0.4224 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.7296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4397 Z= 0.143 Angle : 0.780 17.184 5932 Z= 0.379 Chirality : 0.046 0.234 696 Planarity : 0.005 0.049 750 Dihedral : 4.689 20.595 586 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.58 % Allowed : 25.21 % Favored : 70.21 % 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 are not related in a simple way. whole: 0.23 (0.37), residues: 524 helix: 0.96 (0.33), residues: 243 sheet: 1.45 (0.63), residues: 60 loop : -1.14 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 720 TYR 0.016 0.002 TYR H 610 PHE 0.036 0.002 PHE I 581 TRP 0.010 0.002 TRP H 567 HIS 0.002 0.000 HIS I 565 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4397) covalent geometry : angle 0.77950 ( 5932) hydrogen bonds : bond 0.03585 ( 232) hydrogen bonds : angle 5.08297 ( 657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 558 GLN cc_start: 0.7632 (tt0) cc_final: 0.7353 (pt0) REVERT: J 610 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7360 (mt-10) outliers start: 22 outliers final: 17 residues processed: 138 average time/residue: 0.0791 time to fit residues: 13.5824 Evaluate side-chains 131 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 636 SER Chi-restraints excluded: chain I residue 574 LEU Chi-restraints excluded: chain I residue 605 ILE Chi-restraints excluded: chain I residue 699 THR Chi-restraints excluded: chain I residue 700 LEU Chi-restraints excluded: chain I residue 743 VAL Chi-restraints excluded: chain I residue 744 CYS Chi-restraints excluded: chain J residue 544 PHE Chi-restraints excluded: chain J residue 554 THR Chi-restraints excluded: chain J residue 604 VAL Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 627 TYR Chi-restraints excluded: chain J residue 692 THR Chi-restraints excluded: chain J residue 714 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.5980 chunk 22 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 555 GLN J 595 GLN ** J 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.142925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.129726 restraints weight = 14470.509| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 3.82 r_work: 0.4212 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.7672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4397 Z= 0.146 Angle : 0.817 16.325 5932 Z= 0.392 Chirality : 0.046 0.214 696 Planarity : 0.006 0.074 750 Dihedral : 4.775 20.068 586 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.58 % Allowed : 27.29 % Favored : 68.12 % 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 are not related in a simple way. whole: 0.21 (0.37), residues: 524 helix: 0.97 (0.33), residues: 244 sheet: 1.47 (0.63), residues: 60 loop : -1.20 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 720 TYR 0.019 0.002 TYR H 610 PHE 0.036 0.002 PHE I 581 TRP 0.009 0.001 TRP H 567 HIS 0.002 0.000 HIS I 565 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 4397) covalent geometry : angle 0.81729 ( 5932) hydrogen bonds : bond 0.03541 ( 232) hydrogen bonds : angle 5.14706 ( 657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 512 LYS cc_start: 0.8249 (ttmt) cc_final: 0.8012 (ttmt) REVERT: H 558 GLN cc_start: 0.7797 (tt0) cc_final: 0.7512 (pt0) outliers start: 22 outliers final: 17 residues processed: 138 average time/residue: 0.0749 time to fit residues: 13.0954 Evaluate side-chains 132 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 636 SER Chi-restraints excluded: chain H residue 665 LEU Chi-restraints excluded: chain I residue 574 LEU Chi-restraints excluded: chain I residue 603 THR Chi-restraints excluded: chain I residue 605 ILE Chi-restraints excluded: chain I residue 699 THR Chi-restraints excluded: chain I residue 743 VAL Chi-restraints excluded: chain I residue 744 CYS Chi-restraints excluded: chain J residue 544 PHE Chi-restraints excluded: chain J residue 554 THR Chi-restraints excluded: chain J residue 604 VAL Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 627 TYR Chi-restraints excluded: chain J residue 714 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 555 GLN J 595 GLN J 628 ASN ** J 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.142593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.128373 restraints weight = 14574.154| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 3.71 r_work: 0.4210 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.7927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4397 Z= 0.155 Angle : 0.887 23.323 5932 Z= 0.417 Chirality : 0.047 0.190 696 Planarity : 0.005 0.051 750 Dihedral : 4.776 20.763 586 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 5.62 % Allowed : 26.04 % Favored : 68.33 % 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 are not related in a simple way. whole: 0.17 (0.37), residues: 524 helix: 0.90 (0.33), residues: 243 sheet: 1.53 (0.63), residues: 60 loop : -1.20 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 720 TYR 0.016 0.002 TYR J 624 PHE 0.038 0.002 PHE I 581 TRP 0.008 0.001 TRP H 567 HIS 0.003 0.001 HIS I 565 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 4397) covalent geometry : angle 0.88732 ( 5932) hydrogen bonds : bond 0.03597 ( 232) hydrogen bonds : angle 5.19666 ( 657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 512 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8074 (ttmt) REVERT: H 558 GLN cc_start: 0.7755 (tt0) cc_final: 0.7552 (tm-30) REVERT: J 610 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7424 (mt-10) outliers start: 27 outliers final: 18 residues processed: 136 average time/residue: 0.0708 time to fit residues: 12.2588 Evaluate side-chains 129 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 636 SER Chi-restraints excluded: chain H residue 665 LEU Chi-restraints excluded: chain I residue 574 LEU Chi-restraints excluded: chain I residue 603 THR Chi-restraints excluded: chain I residue 699 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 743 VAL Chi-restraints excluded: chain I residue 744 CYS Chi-restraints excluded: chain I residue 750 VAL Chi-restraints excluded: chain J residue 544 PHE Chi-restraints excluded: chain J residue 554 THR Chi-restraints excluded: chain J residue 604 VAL Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 627 TYR Chi-restraints excluded: chain J residue 714 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 19 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 0.0980 chunk 25 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 595 GLN J 628 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.141793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.129032 restraints weight = 14409.603| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 3.62 r_work: 0.4215 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.8277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4397 Z= 0.150 Angle : 0.874 22.829 5932 Z= 0.416 Chirality : 0.047 0.175 696 Planarity : 0.006 0.084 750 Dihedral : 4.793 20.538 586 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.38 % Allowed : 26.67 % Favored : 68.96 % 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 are not related in a simple way. whole: 0.20 (0.37), residues: 524 helix: 0.97 (0.32), residues: 243 sheet: 1.54 (0.64), residues: 60 loop : -1.24 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 709 TYR 0.021 0.002 TYR H 610 PHE 0.040 0.002 PHE I 581 TRP 0.008 0.001 TRP H 567 HIS 0.003 0.001 HIS I 594 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4397) covalent geometry : angle 0.87358 ( 5932) hydrogen bonds : bond 0.03510 ( 232) hydrogen bonds : angle 5.22784 ( 657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 512 LYS cc_start: 0.8291 (ttmt) cc_final: 0.8059 (ttmt) REVERT: H 531 GLN cc_start: 0.7583 (tp40) cc_final: 0.7371 (pt0) REVERT: H 558 GLN cc_start: 0.7774 (tt0) cc_final: 0.7545 (tm-30) REVERT: H 607 MET cc_start: 0.5238 (mmm) cc_final: 0.4845 (mmm) REVERT: J 610 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7455 (mt-10) REVERT: J 628 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.7136 (t0) outliers start: 21 outliers final: 17 residues processed: 132 average time/residue: 0.0670 time to fit residues: 11.3652 Evaluate side-chains 127 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 470 LEU Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 582 THR Chi-restraints excluded: chain H residue 636 SER Chi-restraints excluded: chain I residue 574 LEU Chi-restraints excluded: chain I residue 699 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 743 VAL Chi-restraints excluded: chain I residue 744 CYS Chi-restraints excluded: chain I residue 750 VAL Chi-restraints excluded: chain J residue 544 PHE Chi-restraints excluded: chain J residue 554 THR Chi-restraints excluded: chain J residue 595 GLN Chi-restraints excluded: chain J residue 604 VAL Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 627 TYR Chi-restraints excluded: chain J residue 628 ASN Chi-restraints excluded: chain J residue 714 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 604 HIS J 595 GLN J 628 ASN ** J 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.141824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.129105 restraints weight = 14700.709| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 3.56 r_work: 0.4223 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.8414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4397 Z= 0.152 Angle : 0.908 22.470 5932 Z= 0.434 Chirality : 0.048 0.216 696 Planarity : 0.006 0.080 750 Dihedral : 4.848 20.499 586 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.96 % Allowed : 28.75 % Favored : 67.29 % 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 are not related in a simple way. whole: 0.19 (0.37), residues: 524 helix: 0.97 (0.33), residues: 243 sheet: 1.60 (0.64), residues: 60 loop : -1.26 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG I 720 TYR 0.027 0.003 TYR I 606 PHE 0.039 0.002 PHE I 581 TRP 0.008 0.001 TRP H 567 HIS 0.002 0.000 HIS I 594 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4397) covalent geometry : angle 0.90849 ( 5932) hydrogen bonds : bond 0.03618 ( 232) hydrogen bonds : angle 5.15071 ( 657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1605.02 seconds wall clock time: 28 minutes 10.47 seconds (1690.47 seconds total)