Starting phenix.real_space_refine on Mon Feb 10 21:33:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2u_44115/02_2025/9b2u_44115_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2u_44115/02_2025/9b2u_44115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b2u_44115/02_2025/9b2u_44115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2u_44115/02_2025/9b2u_44115.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2u_44115/02_2025/9b2u_44115_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2u_44115/02_2025/9b2u_44115_neut.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 15 5.16 5 C 1705 2.51 5 N 456 2.21 5 O 496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2672 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "K" Number of atoms: 2636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2636 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 316} Time building chain proxies: 2.85, per 1000 atoms: 1.07 Number of scatterers: 2672 At special positions: 0 Unit cell: (67.9, 74.69, 61.11, 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 15 16.00 O 496 8.00 N 456 7.00 C 1705 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: 0.62 Conformation dependent library (CDL) restraints added in 375.9 milliseconds 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 626 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 5 sheets defined 42.0% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'K' and resid 474 through 479 removed outlier: 4.039A pdb=" N CYS K 478 " --> pdb=" O PRO K 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 480 through 486 removed outlier: 3.537A pdb=" N ARG K 486 " --> pdb=" O GLU K 482 " (cutoff:3.500A) Processing helix chain 'K' and resid 528 through 545 Proline residue: K 534 - end of helix removed outlier: 3.537A pdb=" N LEU K 545 " --> pdb=" O GLU K 541 " (cutoff:3.500A) Processing helix chain 'K' and resid 546 through 548 No H-bonds generated for 'chain 'K' and resid 546 through 548' Processing helix chain 'K' and resid 570 through 584 removed outlier: 3.534A pdb=" N LEU K 574 " --> pdb=" O PRO K 570 " (cutoff:3.500A) Processing helix chain 'K' and resid 613 through 615 No H-bonds generated for 'chain 'K' and resid 613 through 615' Processing helix chain 'K' and resid 621 through 644 Processing helix chain 'K' and resid 708 through 713 removed outlier: 3.541A pdb=" N THR K 712 " --> pdb=" O ASP K 709 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY K 713 " --> pdb=" O LEU K 710 " (cutoff:3.500A) Processing helix chain 'K' and resid 716 through 729 removed outlier: 4.020A pdb=" N TYR K 722 " --> pdb=" O GLN K 718 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG K 723 " --> pdb=" O PHE K 719 " (cutoff:3.500A) Processing helix chain 'K' and resid 738 through 755 removed outlier: 4.049A pdb=" N VAL K 742 " --> pdb=" O PRO K 738 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU K 743 " --> pdb=" O TYR K 739 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP K 744 " --> pdb=" O SER K 740 " (cutoff:3.500A) Processing helix chain 'K' and resid 764 through 780 Processing helix chain 'K' and resid 786 through 794 Processing sheet with id=AA1, first strand: chain 'K' and resid 472 through 473 removed outlier: 6.047A pdb=" N VAL K 473 " --> pdb=" O GLN K 566 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LEU K 559 " --> pdb=" O GLU K 606 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLU K 606 " --> pdb=" O LEU K 559 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER K 561 " --> pdb=" O GLU K 604 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS K 563 " --> pdb=" O VAL K 602 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU K 599 " --> pdb=" O ILE K 515 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE K 515 " --> pdb=" O LEU K 599 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY K 496 " --> pdb=" O GLU K 492 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU K 492 " --> pdb=" O GLY K 496 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL K 498 " --> pdb=" O ILE K 490 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 520 through 521 Processing sheet with id=AA3, first strand: chain 'K' and resid 610 through 611 removed outlier: 3.501A pdb=" N ILE K 610 " --> pdb=" O LEU K 657 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 664 through 669 Processing sheet with id=AA5, first strand: chain 'K' and resid 693 through 695 117 hydrogen bonds defined for protein. 333 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: 0.72 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 864 1.34 - 1.46: 602 1.46 - 1.58: 1242 1.58 - 1.70: 0 1.70 - 1.81: 22 Bond restraints: 2730 Sorted by residual: bond pdb=" N LYS E 4 " pdb=" CA LYS E 4 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.21e-02 6.83e+03 6.71e+00 bond pdb=" N THR E 3 " pdb=" CA THR E 3 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.84e+00 bond pdb=" N ARG E 2 " pdb=" CA ARG E 2 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.59e+00 bond pdb=" N GLN E 5 " pdb=" CA GLN E 5 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.48e+00 bond pdb=" CB ASP K 696 " pdb=" CG ASP K 696 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.99e+00 ... (remaining 2725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 3538 1.71 - 3.41: 121 3.41 - 5.12: 14 5.12 - 6.83: 6 6.83 - 8.54: 4 Bond angle restraints: 3683 Sorted by residual: angle pdb=" CA LYS K 489 " pdb=" CB LYS K 489 " pdb=" CG LYS K 489 " ideal model delta sigma weight residual 114.10 120.96 -6.86 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CA GLU K 606 " pdb=" CB GLU K 606 " pdb=" CG GLU K 606 " ideal model delta sigma weight residual 114.10 120.07 -5.97 2.00e+00 2.50e-01 8.90e+00 angle pdb=" C THR K 528 " pdb=" CA THR K 528 " pdb=" CB THR K 528 " ideal model delta sigma weight residual 109.66 115.16 -5.50 1.94e+00 2.66e-01 8.03e+00 angle pdb=" CA LEU K 484 " pdb=" CB LEU K 484 " pdb=" CG LEU K 484 " ideal model delta sigma weight residual 116.30 124.84 -8.54 3.50e+00 8.16e-02 5.95e+00 angle pdb=" N PHE K 529 " pdb=" CA PHE K 529 " pdb=" C PHE K 529 " ideal model delta sigma weight residual 111.28 113.87 -2.59 1.09e+00 8.42e-01 5.64e+00 ... (remaining 3678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 1375 17.84 - 35.68: 211 35.68 - 53.52: 46 53.52 - 71.36: 5 71.36 - 89.20: 7 Dihedral angle restraints: 1644 sinusoidal: 678 harmonic: 966 Sorted by residual: dihedral pdb=" CA HIS K 647 " pdb=" C HIS K 647 " pdb=" N ARG K 648 " pdb=" CA ARG K 648 " ideal model delta harmonic sigma weight residual 180.00 157.74 22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA PHE K 593 " pdb=" C PHE K 593 " pdb=" N PHE K 594 " pdb=" CA PHE K 594 " ideal model delta harmonic sigma weight residual -180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA LEU K 650 " pdb=" C LEU K 650 " pdb=" N HIS K 651 " pdb=" CA HIS K 651 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 1641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 211 0.027 - 0.053: 106 0.053 - 0.080: 56 0.080 - 0.107: 28 0.107 - 0.133: 9 Chirality restraints: 410 Sorted by residual: chirality pdb=" CA ILE K 515 " pdb=" N ILE K 515 " pdb=" C ILE K 515 " pdb=" CB ILE K 515 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE K 513 " pdb=" N ILE K 513 " pdb=" C ILE K 513 " pdb=" CB ILE K 513 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ASN K 730 " pdb=" N ASN K 730 " pdb=" C ASN K 730 " pdb=" CB ASN K 730 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 407 not shown) Planarity restraints: 468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP K 696 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.69e+00 pdb=" C ASP K 696 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP K 696 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY K 697 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 577 " -0.016 2.00e-02 2.50e+03 1.18e-02 3.48e+00 pdb=" CG TRP K 577 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP K 577 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP K 577 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP K 577 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP K 577 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP K 577 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 577 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 577 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP K 577 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 722 " 0.014 2.00e-02 2.50e+03 1.15e-02 2.64e+00 pdb=" CG TYR K 722 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR K 722 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR K 722 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR K 722 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR K 722 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR K 722 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR K 722 " 0.000 2.00e-02 2.50e+03 ... (remaining 465 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 75 2.70 - 3.25: 2729 3.25 - 3.80: 4074 3.80 - 4.35: 5227 4.35 - 4.90: 8389 Nonbonded interactions: 20494 Sorted by model distance: nonbonded pdb=" OG SER K 546 " pdb=" O THR K 553 " model vdw 2.144 3.040 nonbonded pdb=" O SER K 621 " pdb=" OG1 THR K 624 " model vdw 2.206 3.040 nonbonded pdb=" OE2 GLU K 640 " pdb=" ND2 ASN K 741 " model vdw 2.231 3.120 nonbonded pdb=" O VAL K 562 " pdb=" ND1 HIS K 563 " model vdw 2.246 3.120 nonbonded pdb=" N ASP K 709 " pdb=" OD1 ASP K 709 " model vdw 2.342 3.120 ... (remaining 20489 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 group one per residue 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: 2.660 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.110 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5589 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 : 0.003 0.036 2730 Z= 0.219 Angle : 0.777 8.536 3683 Z= 0.420 Chirality : 0.045 0.133 410 Planarity : 0.003 0.022 468 Dihedral : 17.956 89.198 1018 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.67 % Allowed : 30.67 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.45), residues: 329 helix: 0.43 (0.49), residues: 111 sheet: 1.27 (0.73), residues: 52 loop : -1.42 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP K 577 HIS 0.003 0.001 HIS K 651 PHE 0.018 0.002 PHE K 594 TYR 0.028 0.002 TYR K 722 ARG 0.001 0.000 ARG K 590 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: K 552 ARG cc_start: 0.6882 (ttm110) cc_final: 0.6329 (ttp80) REVERT: K 572 LEU cc_start: 0.6421 (mp) cc_final: 0.6128 (mp) REVERT: K 644 ARG cc_start: 0.6542 (ttm170) cc_final: 0.5534 (ttm110) REVERT: K 738 PRO cc_start: 0.7661 (Cg_endo) cc_final: 0.7407 (Cg_exo) outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.1914 time to fit residues: 12.7173 Evaluate side-chains 41 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 709 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.0170 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.0570 chunk 19 optimal weight: 0.1980 chunk 29 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.1736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 5 GLN K 500 GLN K 737 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.226294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.199476 restraints weight = 3475.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.200918 restraints weight = 2256.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.203053 restraints weight = 1860.520| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2730 Z= 0.160 Angle : 0.634 7.914 3683 Z= 0.318 Chirality : 0.045 0.149 410 Planarity : 0.003 0.028 468 Dihedral : 4.741 18.132 356 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 7.33 % Allowed : 24.67 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.46), residues: 329 helix: 0.62 (0.50), residues: 117 sheet: 1.74 (0.73), residues: 52 loop : -1.52 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 577 HIS 0.002 0.001 HIS K 651 PHE 0.008 0.001 PHE K 719 TYR 0.017 0.002 TYR K 722 ARG 0.001 0.000 ARG K 723 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 41 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6209 (mp) cc_final: 0.5851 (mt) REVERT: K 688 TYR cc_start: 0.5425 (OUTLIER) cc_final: 0.5179 (m-80) REVERT: K 700 VAL cc_start: 0.6966 (OUTLIER) cc_final: 0.6714 (t) REVERT: K 706 MET cc_start: 0.3831 (OUTLIER) cc_final: 0.2128 (ptp) outliers start: 22 outliers final: 4 residues processed: 61 average time/residue: 0.1645 time to fit residues: 11.8357 Evaluate side-chains 43 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 528 THR Chi-restraints excluded: chain K residue 579 HIS Chi-restraints excluded: chain K residue 669 LEU Chi-restraints excluded: chain K residue 684 SER Chi-restraints excluded: chain K residue 688 TYR Chi-restraints excluded: chain K residue 700 VAL Chi-restraints excluded: chain K residue 706 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.0980 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.219446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.191649 restraints weight = 3514.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.192471 restraints weight = 2476.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.195362 restraints weight = 1849.131| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2730 Z= 0.225 Angle : 0.632 9.629 3683 Z= 0.320 Chirality : 0.044 0.133 410 Planarity : 0.004 0.039 468 Dihedral : 4.773 15.405 354 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 7.00 % Allowed : 20.67 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.46), residues: 329 helix: 0.36 (0.50), residues: 117 sheet: 1.28 (0.69), residues: 60 loop : -1.62 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP K 577 HIS 0.003 0.001 HIS K 651 PHE 0.016 0.001 PHE K 594 TYR 0.016 0.002 TYR K 580 ARG 0.003 0.000 ARG K 772 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.6017 (mt) REVERT: K 706 MET cc_start: 0.4270 (OUTLIER) cc_final: 0.2486 (ptp) outliers start: 21 outliers final: 9 residues processed: 55 average time/residue: 0.1299 time to fit residues: 8.8836 Evaluate side-chains 50 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 510 ILE Chi-restraints excluded: chain K residue 528 THR Chi-restraints excluded: chain K residue 572 LEU Chi-restraints excluded: chain K residue 579 HIS Chi-restraints excluded: chain K residue 593 PHE Chi-restraints excluded: chain K residue 669 LEU Chi-restraints excluded: chain K residue 678 SER Chi-restraints excluded: chain K residue 699 VAL Chi-restraints excluded: chain K residue 706 MET Chi-restraints excluded: chain K residue 750 ASP Chi-restraints excluded: chain K residue 760 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.215307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.186743 restraints weight = 3574.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.188183 restraints weight = 2655.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.190382 restraints weight = 1975.977| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2730 Z= 0.243 Angle : 0.652 9.790 3683 Z= 0.334 Chirality : 0.045 0.131 410 Planarity : 0.005 0.037 468 Dihedral : 4.910 15.727 354 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 6.00 % Allowed : 22.67 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.46), residues: 329 helix: 0.26 (0.48), residues: 117 sheet: 1.03 (0.68), residues: 60 loop : -1.84 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP K 577 HIS 0.003 0.001 HIS K 647 PHE 0.010 0.002 PHE K 594 TYR 0.017 0.002 TYR K 580 ARG 0.002 0.001 ARG K 590 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5900 (mt) REVERT: K 616 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7820 (mtm110) REVERT: K 672 LYS cc_start: 0.5667 (tppt) cc_final: 0.4600 (ptpt) REVERT: K 688 TYR cc_start: 0.5469 (OUTLIER) cc_final: 0.5226 (m-10) REVERT: K 706 MET cc_start: 0.4512 (OUTLIER) cc_final: 0.2602 (ptp) outliers start: 18 outliers final: 9 residues processed: 54 average time/residue: 0.1537 time to fit residues: 9.9841 Evaluate side-chains 53 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 510 ILE Chi-restraints excluded: chain K residue 528 THR Chi-restraints excluded: chain K residue 572 LEU Chi-restraints excluded: chain K residue 579 HIS Chi-restraints excluded: chain K residue 593 PHE Chi-restraints excluded: chain K residue 604 GLU Chi-restraints excluded: chain K residue 616 ARG Chi-restraints excluded: chain K residue 629 LEU Chi-restraints excluded: chain K residue 669 LEU Chi-restraints excluded: chain K residue 688 TYR Chi-restraints excluded: chain K residue 706 MET Chi-restraints excluded: chain K residue 750 ASP Chi-restraints excluded: chain K residue 783 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.215979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.187766 restraints weight = 3537.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.188653 restraints weight = 3024.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.190503 restraints weight = 2124.792| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2730 Z= 0.198 Angle : 0.577 8.929 3683 Z= 0.298 Chirality : 0.043 0.126 410 Planarity : 0.004 0.034 468 Dihedral : 4.666 14.791 354 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 7.67 % Allowed : 23.00 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.46), residues: 329 helix: 0.49 (0.50), residues: 117 sheet: 1.03 (0.69), residues: 60 loop : -1.74 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP K 577 HIS 0.003 0.001 HIS K 651 PHE 0.012 0.001 PHE K 594 TYR 0.016 0.002 TYR K 580 ARG 0.003 0.000 ARG K 590 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.5878 (mt) REVERT: K 616 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7899 (mtm110) REVERT: K 672 LYS cc_start: 0.5701 (tppt) cc_final: 0.4607 (ptpt) REVERT: K 706 MET cc_start: 0.4529 (OUTLIER) cc_final: 0.2780 (ptp) REVERT: K 745 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.5976 (mm) outliers start: 23 outliers final: 11 residues processed: 61 average time/residue: 0.1501 time to fit residues: 11.1087 Evaluate side-chains 56 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 510 ILE Chi-restraints excluded: chain K residue 524 SER Chi-restraints excluded: chain K residue 528 THR Chi-restraints excluded: chain K residue 572 LEU Chi-restraints excluded: chain K residue 579 HIS Chi-restraints excluded: chain K residue 593 PHE Chi-restraints excluded: chain K residue 604 GLU Chi-restraints excluded: chain K residue 616 ARG Chi-restraints excluded: chain K residue 629 LEU Chi-restraints excluded: chain K residue 669 LEU Chi-restraints excluded: chain K residue 678 SER Chi-restraints excluded: chain K residue 706 MET Chi-restraints excluded: chain K residue 745 LEU Chi-restraints excluded: chain K residue 750 ASP Chi-restraints excluded: chain K residue 760 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 2 optimal weight: 0.0060 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.216752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.190155 restraints weight = 3654.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.191057 restraints weight = 2301.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.191605 restraints weight = 2183.742| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2730 Z= 0.166 Angle : 0.562 8.644 3683 Z= 0.285 Chirality : 0.043 0.132 410 Planarity : 0.004 0.037 468 Dihedral : 4.511 14.119 354 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 6.33 % Allowed : 25.00 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.46), residues: 329 helix: 0.46 (0.50), residues: 117 sheet: 1.02 (0.69), residues: 60 loop : -1.73 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 577 HIS 0.003 0.001 HIS K 651 PHE 0.007 0.001 PHE K 784 TYR 0.014 0.001 TYR K 580 ARG 0.004 0.000 ARG K 779 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6274 (mt) REVERT: K 577 TRP cc_start: 0.5663 (t60) cc_final: 0.5455 (t60) REVERT: K 616 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7894 (mtm110) REVERT: K 672 LYS cc_start: 0.5787 (tppt) cc_final: 0.4669 (ptpt) REVERT: K 706 MET cc_start: 0.4521 (OUTLIER) cc_final: 0.2831 (ptp) outliers start: 19 outliers final: 11 residues processed: 54 average time/residue: 0.1304 time to fit residues: 8.7202 Evaluate side-chains 54 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 510 ILE Chi-restraints excluded: chain K residue 524 SER Chi-restraints excluded: chain K residue 528 THR Chi-restraints excluded: chain K residue 572 LEU Chi-restraints excluded: chain K residue 579 HIS Chi-restraints excluded: chain K residue 593 PHE Chi-restraints excluded: chain K residue 604 GLU Chi-restraints excluded: chain K residue 616 ARG Chi-restraints excluded: chain K residue 629 LEU Chi-restraints excluded: chain K residue 669 LEU Chi-restraints excluded: chain K residue 678 SER Chi-restraints excluded: chain K residue 706 MET Chi-restraints excluded: chain K residue 750 ASP Chi-restraints excluded: chain K residue 760 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 19 optimal weight: 0.2980 chunk 3 optimal weight: 0.0980 overall best weight: 0.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.218359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.191288 restraints weight = 3672.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.191510 restraints weight = 2567.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.191798 restraints weight = 2279.773| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2730 Z= 0.142 Angle : 0.526 8.096 3683 Z= 0.266 Chirality : 0.042 0.131 410 Planarity : 0.004 0.035 468 Dihedral : 4.282 13.803 354 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 7.67 % Allowed : 23.33 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.47), residues: 329 helix: 0.55 (0.51), residues: 117 sheet: 1.11 (0.69), residues: 60 loop : -1.65 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 577 HIS 0.003 0.001 HIS K 651 PHE 0.006 0.001 PHE K 784 TYR 0.014 0.001 TYR K 580 ARG 0.004 0.000 ARG K 779 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.6076 (mt) REVERT: K 577 TRP cc_start: 0.5806 (t60) cc_final: 0.5601 (t60) REVERT: K 616 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7843 (mtm110) REVERT: K 672 LYS cc_start: 0.5620 (tppt) cc_final: 0.4666 (ptpt) REVERT: K 706 MET cc_start: 0.4501 (OUTLIER) cc_final: 0.2812 (ptp) REVERT: K 745 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.6129 (mm) outliers start: 23 outliers final: 12 residues processed: 58 average time/residue: 0.1276 time to fit residues: 9.1955 Evaluate side-chains 55 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 510 ILE Chi-restraints excluded: chain K residue 524 SER Chi-restraints excluded: chain K residue 528 THR Chi-restraints excluded: chain K residue 572 LEU Chi-restraints excluded: chain K residue 579 HIS Chi-restraints excluded: chain K residue 604 GLU Chi-restraints excluded: chain K residue 616 ARG Chi-restraints excluded: chain K residue 629 LEU Chi-restraints excluded: chain K residue 669 LEU Chi-restraints excluded: chain K residue 678 SER Chi-restraints excluded: chain K residue 706 MET Chi-restraints excluded: chain K residue 721 ILE Chi-restraints excluded: chain K residue 745 LEU Chi-restraints excluded: chain K residue 750 ASP Chi-restraints excluded: chain K residue 752 MET Chi-restraints excluded: chain K residue 760 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.0870 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.0570 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.0670 chunk 22 optimal weight: 0.0980 overall best weight: 0.0812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 563 HIS K 651 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.221787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.193987 restraints weight = 3557.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.195008 restraints weight = 2522.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.197952 restraints weight = 1811.587| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2730 Z= 0.118 Angle : 0.537 9.169 3683 Z= 0.264 Chirality : 0.041 0.131 410 Planarity : 0.004 0.036 468 Dihedral : 4.037 14.516 354 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.67 % Allowed : 26.67 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.47), residues: 329 helix: 0.74 (0.51), residues: 117 sheet: 1.27 (0.70), residues: 60 loop : -1.57 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 577 HIS 0.002 0.000 HIS K 651 PHE 0.006 0.001 PHE K 499 TYR 0.013 0.001 TYR K 580 ARG 0.003 0.000 ARG K 779 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.5972 (mt) REVERT: K 672 LYS cc_start: 0.5325 (tppt) cc_final: 0.4441 (ptpt) REVERT: K 706 MET cc_start: 0.4110 (OUTLIER) cc_final: 0.2879 (ptp) REVERT: K 745 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.6037 (mm) REVERT: K 756 MET cc_start: 0.7779 (mmt) cc_final: 0.7519 (mmt) outliers start: 11 outliers final: 5 residues processed: 48 average time/residue: 0.1215 time to fit residues: 7.4075 Evaluate side-chains 47 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 510 ILE Chi-restraints excluded: chain K residue 572 LEU Chi-restraints excluded: chain K residue 579 HIS Chi-restraints excluded: chain K residue 629 LEU Chi-restraints excluded: chain K residue 706 MET Chi-restraints excluded: chain K residue 745 LEU Chi-restraints excluded: chain K residue 750 ASP Chi-restraints excluded: chain K residue 760 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 15 optimal weight: 0.0370 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 31 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 0.0370 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.220176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.193217 restraints weight = 3599.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.192971 restraints weight = 2657.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.194377 restraints weight = 2173.675| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2730 Z= 0.137 Angle : 0.558 8.915 3683 Z= 0.271 Chirality : 0.043 0.158 410 Planarity : 0.004 0.035 468 Dihedral : 4.022 13.046 354 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.33 % Allowed : 26.67 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.47), residues: 329 helix: 0.74 (0.50), residues: 117 sheet: 1.37 (0.70), residues: 60 loop : -1.50 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 577 HIS 0.004 0.001 HIS K 651 PHE 0.015 0.001 PHE K 711 TYR 0.012 0.001 TYR K 580 ARG 0.002 0.000 ARG K 779 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6037 (mt) REVERT: K 672 LYS cc_start: 0.5562 (tppt) cc_final: 0.4646 (ptpt) REVERT: K 745 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.6139 (mm) outliers start: 13 outliers final: 8 residues processed: 47 average time/residue: 0.1303 time to fit residues: 7.7772 Evaluate side-chains 48 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 510 ILE Chi-restraints excluded: chain K residue 524 SER Chi-restraints excluded: chain K residue 572 LEU Chi-restraints excluded: chain K residue 579 HIS Chi-restraints excluded: chain K residue 604 GLU Chi-restraints excluded: chain K residue 629 LEU Chi-restraints excluded: chain K residue 745 LEU Chi-restraints excluded: chain K residue 750 ASP Chi-restraints excluded: chain K residue 752 MET Chi-restraints excluded: chain K residue 776 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 4 optimal weight: 0.4980 chunk 13 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 2 optimal weight: 0.0010 chunk 7 optimal weight: 0.8980 overall best weight: 0.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.217466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.191150 restraints weight = 3662.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.190099 restraints weight = 2463.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.191762 restraints weight = 2530.767| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2730 Z= 0.163 Angle : 0.577 8.851 3683 Z= 0.284 Chirality : 0.043 0.143 410 Planarity : 0.004 0.036 468 Dihedral : 4.223 12.439 354 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.00 % Allowed : 27.33 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.47), residues: 329 helix: 0.60 (0.50), residues: 117 sheet: 1.44 (0.71), residues: 59 loop : -1.56 (0.48), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 577 HIS 0.005 0.001 HIS K 651 PHE 0.019 0.001 PHE K 711 TYR 0.012 0.001 TYR K 580 ARG 0.002 0.000 ARG K 779 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6146 (mt) REVERT: K 672 LYS cc_start: 0.5705 (tppt) cc_final: 0.4736 (ptpt) REVERT: K 745 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.6096 (mm) outliers start: 12 outliers final: 9 residues processed: 48 average time/residue: 0.1179 time to fit residues: 7.1551 Evaluate side-chains 48 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 510 ILE Chi-restraints excluded: chain K residue 524 SER Chi-restraints excluded: chain K residue 572 LEU Chi-restraints excluded: chain K residue 579 HIS Chi-restraints excluded: chain K residue 629 LEU Chi-restraints excluded: chain K residue 678 SER Chi-restraints excluded: chain K residue 745 LEU Chi-restraints excluded: chain K residue 750 ASP Chi-restraints excluded: chain K residue 752 MET Chi-restraints excluded: chain K residue 760 THR Chi-restraints excluded: chain K residue 776 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.0470 chunk 13 optimal weight: 0.7980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 525 HIS K 563 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.218343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.190451 restraints weight = 3582.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.193705 restraints weight = 2233.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.195522 restraints weight = 1628.416| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2730 Z= 0.187 Angle : 0.598 8.605 3683 Z= 0.297 Chirality : 0.044 0.142 410 Planarity : 0.004 0.035 468 Dihedral : 4.488 16.442 354 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.33 % Allowed : 26.67 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.47), residues: 329 helix: 0.39 (0.49), residues: 117 sheet: 1.45 (0.72), residues: 59 loop : -1.61 (0.48), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP K 577 HIS 0.005 0.001 HIS K 651 PHE 0.018 0.002 PHE K 711 TYR 0.013 0.001 TYR K 580 ARG 0.002 0.000 ARG K 779 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1394.71 seconds wall clock time: 25 minutes 47.11 seconds (1547.11 seconds total)