Starting phenix.real_space_refine on Wed Mar 5 16:29:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2u_44115/03_2025/9b2u_44115_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2u_44115/03_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_44115/03_2025/9b2u_44115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2u_44115/03_2025/9b2u_44115.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2u_44115/03_2025/9b2u_44115_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2u_44115/03_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-5624/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: 4.57, per 1000 atoms: 1.71 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: 0.68 Conformation dependent library (CDL) restraints added in 286.2 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: 0.75 Time building geometry restraints manager: 0.80 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: 9.620 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: 14.040 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- 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 : 0.290 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: 0.1763 time to fit residues: 11.6793 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 : 0.317 ------------------------------------------------------------------------------- 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: 0.1980 chunk 19 optimal weight: 0.1980 chunk 29 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.1816 ------------------------------------------------------------------------------- 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 = 0.4469 r_free = 0.4469 target = 0.225957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.198991 restraints weight = 3468.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.200676 restraints weight = 2278.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.202696 restraints weight = 1741.741| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.1619 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= 0.163 Angle : 0.636 8.069 3683 Z= 0.319 Chirality : 0.045 0.165 410 Planarity : 0.003 0.028 468 Dihedral : 4.745 18.112 356 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 7.00 % Allowed : 24.33 % 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: -0.28 (0.46), residues: 329 helix: 0.62 (0.50), residues: 117 sheet: 1.72 (0.73), residues: 52 loop : -1.52 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 577 HIS 0.003 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 62 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6211 (mp) cc_final: 0.5845 (mt) REVERT: K 688 TYR cc_start: 0.5439 (OUTLIER) cc_final: 0.5166 (m-80) REVERT: K 700 VAL cc_start: 0.6979 (OUTLIER) cc_final: 0.6713 (t) REVERT: K 706 MET cc_start: 0.3873 (OUTLIER) cc_final: 0.2136 (ptp) outliers start: 21 outliers final: 3 residues processed: 60 average time/residue: 0.1746 time to fit residues: 12.3860 Evaluate side-chains 41 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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: 0.0870 chunk 14 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 overall best weight: 0.3558 ------------------------------------------------------------------------------- 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 = 0.4431 r_free = 0.4431 target = 0.221404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.193511 restraints weight = 3505.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.193998 restraints weight = 2558.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.197413 restraints weight = 1808.242| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2730 Z= 0.192 Angle : 0.616 9.280 3683 Z= 0.309 Chirality : 0.044 0.130 410 Planarity : 0.004 0.034 468 Dihedral : 4.658 15.256 354 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 7.00 % Allowed : 21.33 % 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 (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: -0.45 (0.46), residues: 329 helix: 0.40 (0.50), residues: 117 sheet: 1.32 (0.69), residues: 60 loop : -1.58 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 577 HIS 0.003 0.001 HIS K 651 PHE 0.011 0.001 PHE K 594 TYR 0.016 0.002 TYR K 580 ARG 0.002 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 : 0.282 Fit side-chains revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.5925 (mt) REVERT: K 706 MET cc_start: 0.4274 (OUTLIER) cc_final: 0.2503 (ptp) outliers start: 21 outliers final: 9 residues processed: 55 average time/residue: 0.1245 time to fit residues: 8.5481 Evaluate side-chains 51 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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: 0.7980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4346 r_free = 0.4346 target = 0.212403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.183631 restraints weight = 3573.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.184393 restraints weight = 2841.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.186887 restraints weight = 2052.541| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2730 Z= 0.289 Angle : 0.713 10.624 3683 Z= 0.365 Chirality : 0.047 0.135 410 Planarity : 0.005 0.029 468 Dihedral : 5.164 17.178 354 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 6.67 % Allowed : 21.67 % 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 (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: -0.87 (0.45), residues: 329 helix: 0.18 (0.48), residues: 116 sheet: 0.97 (0.67), residues: 60 loop : -1.87 (0.46), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP K 577 HIS 0.004 0.001 HIS K 746 PHE 0.012 0.002 PHE K 593 TYR 0.018 0.002 TYR K 580 ARG 0.003 0.001 ARG K 648 *********************** 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 60 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5749 (mt) REVERT: K 616 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7735 (mtp-110) REVERT: K 672 LYS cc_start: 0.5714 (tppt) cc_final: 0.4696 (ptpt) REVERT: K 688 TYR cc_start: 0.5405 (OUTLIER) cc_final: 0.5125 (m-10) REVERT: K 743 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6252 (mp) outliers start: 20 outliers final: 11 residues processed: 56 average time/residue: 0.1583 time to fit residues: 10.7791 Evaluate side-chains 53 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 688 TYR Chi-restraints excluded: chain K residue 743 LEU 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: 1.9990 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.0060 chunk 20 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 10 optimal weight: 0.0770 chunk 31 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3954 ------------------------------------------------------------------------------- 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 = 0.4368 r_free = 0.4368 target = 0.215007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.186450 restraints weight = 3555.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.187668 restraints weight = 2780.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.189799 restraints weight = 1945.897| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2730 Z= 0.203 Angle : 0.592 9.186 3683 Z= 0.307 Chirality : 0.043 0.126 410 Planarity : 0.004 0.038 468 Dihedral : 4.824 15.303 354 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 6.33 % Allowed : 23.00 % Favored : 70.67 % 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: -0.74 (0.46), residues: 329 helix: 0.33 (0.49), residues: 116 sheet: 0.99 (0.69), residues: 60 loop : -1.81 (0.46), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP K 577 HIS 0.003 0.001 HIS K 651 PHE 0.011 0.001 PHE K 594 TYR 0.015 0.001 TYR K 580 ARG 0.002 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 57 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5777 (mt) REVERT: K 616 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7936 (mtm110) REVERT: K 672 LYS cc_start: 0.5716 (tppt) cc_final: 0.4650 (ptpt) REVERT: K 745 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.6066 (mm) outliers start: 19 outliers final: 11 residues processed: 54 average time/residue: 0.1567 time to fit residues: 10.1805 Evaluate side-chains 50 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 545 LEU 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 721 ILE Chi-restraints excluded: chain K residue 745 LEU Chi-restraints excluded: chain K residue 750 ASP 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: 0.7980 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.0060 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.4338 r_free = 0.4338 target = 0.211807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.183846 restraints weight = 3655.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.182892 restraints weight = 3267.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.185777 restraints weight = 2450.449| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.4161 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= 0.228 Angle : 0.624 9.772 3683 Z= 0.319 Chirality : 0.045 0.138 410 Planarity : 0.004 0.033 468 Dihedral : 4.851 15.787 354 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 6.67 % Allowed : 25.33 % 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: -0.85 (0.46), residues: 329 helix: 0.31 (0.49), residues: 116 sheet: 0.91 (0.71), residues: 60 loop : -1.93 (0.45), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP K 577 HIS 0.003 0.001 HIS K 746 PHE 0.013 0.001 PHE K 594 TYR 0.018 0.002 TYR K 580 ARG 0.004 0.001 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: 20 poor density : 39 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5753 (mt) REVERT: K 672 LYS cc_start: 0.5574 (tppt) cc_final: 0.4665 (ptpt) REVERT: K 745 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.6065 (mm) outliers start: 20 outliers final: 12 residues processed: 54 average time/residue: 0.1381 time to fit residues: 9.1276 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 : 0.314 ------------------------------------------------------------------------------- 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 545 LEU 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 629 LEU Chi-restraints excluded: chain K residue 669 LEU Chi-restraints excluded: chain K residue 699 VAL Chi-restraints excluded: chain K residue 721 ILE Chi-restraints excluded: chain K residue 745 LEU Chi-restraints excluded: chain K residue 750 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.0030 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 overall best weight: 0.3590 ------------------------------------------------------------------------------- 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 = 0.4354 r_free = 0.4354 target = 0.213235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.185452 restraints weight = 3633.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.186171 restraints weight = 2598.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.189057 restraints weight = 1864.319| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.4355 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= 0.188 Angle : 0.585 8.829 3683 Z= 0.297 Chirality : 0.043 0.130 410 Planarity : 0.004 0.036 468 Dihedral : 4.675 14.755 354 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.67 % Allowed : 27.33 % Favored : 67.00 % 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: -0.76 (0.46), residues: 329 helix: 0.42 (0.50), residues: 116 sheet: 0.91 (0.72), residues: 60 loop : -1.89 (0.46), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP K 577 HIS 0.003 0.001 HIS K 794 PHE 0.008 0.001 PHE K 784 TYR 0.014 0.001 TYR K 580 ARG 0.003 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 57 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6028 (mt) REVERT: K 672 LYS cc_start: 0.5839 (tppt) cc_final: 0.4728 (ptpt) REVERT: K 745 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.6115 (mm) outliers start: 17 outliers final: 11 residues processed: 52 average time/residue: 0.1500 time to fit residues: 9.7483 Evaluate side-chains 52 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 545 LEU 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 629 LEU Chi-restraints excluded: chain K residue 669 LEU Chi-restraints excluded: chain K residue 699 VAL Chi-restraints excluded: chain K residue 721 ILE Chi-restraints excluded: chain K residue 745 LEU Chi-restraints excluded: chain K residue 750 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 18 optimal weight: 0.0980 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 overall best weight: 0.2780 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.215463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.189216 restraints weight = 3577.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.189662 restraints weight = 2249.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.191506 restraints weight = 1975.347| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.4509 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= 0.157 Angle : 0.552 8.390 3683 Z= 0.280 Chirality : 0.042 0.131 410 Planarity : 0.004 0.036 468 Dihedral : 4.385 14.208 354 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.33 % Allowed : 26.67 % 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: -0.58 (0.47), residues: 329 helix: 0.51 (0.50), residues: 116 sheet: 1.08 (0.72), residues: 60 loop : -1.75 (0.47), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 577 HIS 0.003 0.001 HIS K 651 PHE 0.007 0.001 PHE K 593 TYR 0.013 0.001 TYR K 580 ARG 0.002 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 56 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6247 (mt) REVERT: K 672 LYS cc_start: 0.5709 (tppt) cc_final: 0.4628 (ptpt) outliers start: 16 outliers final: 11 residues processed: 51 average time/residue: 0.1235 time to fit residues: 7.9203 Evaluate side-chains 50 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 593 PHE Chi-restraints excluded: chain K residue 604 GLU Chi-restraints excluded: chain K residue 629 LEU Chi-restraints excluded: chain K residue 669 LEU Chi-restraints excluded: chain K residue 699 VAL Chi-restraints excluded: chain K residue 721 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4345 r_free = 0.4345 target = 0.212289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.184703 restraints weight = 3644.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.185419 restraints weight = 2831.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.187594 restraints weight = 2147.849| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2730 Z= 0.208 Angle : 0.627 9.527 3683 Z= 0.312 Chirality : 0.044 0.133 410 Planarity : 0.004 0.035 468 Dihedral : 4.619 14.776 354 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.00 % Allowed : 25.33 % 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: -0.69 (0.46), residues: 329 helix: 0.44 (0.49), residues: 116 sheet: 1.03 (0.70), residues: 59 loop : -1.83 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 577 HIS 0.006 0.001 HIS K 651 PHE 0.009 0.001 PHE K 593 TYR 0.014 0.002 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 55 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 572 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6014 (mt) REVERT: K 672 LYS cc_start: 0.5716 (tppt) cc_final: 0.4703 (ptpt) REVERT: K 745 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.6116 (mm) outliers start: 15 outliers final: 11 residues processed: 51 average time/residue: 0.1283 time to fit residues: 8.1404 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 : 0.299 ------------------------------------------------------------------------------- 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 593 PHE Chi-restraints excluded: chain K residue 604 GLU Chi-restraints excluded: chain K residue 629 LEU Chi-restraints excluded: chain K residue 669 LEU Chi-restraints excluded: chain K residue 699 VAL 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 776 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 16 optimal weight: 0.0370 chunk 12 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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 = 0.4343 r_free = 0.4343 target = 0.211925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.185707 restraints weight = 3697.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.186337 restraints weight = 2858.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.188884 restraints weight = 2204.563| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.4850 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= 0.202 Angle : 0.632 9.054 3683 Z= 0.313 Chirality : 0.045 0.157 410 Planarity : 0.004 0.035 468 Dihedral : 4.595 14.740 354 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.67 % Allowed : 25.67 % 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: -0.71 (0.46), residues: 329 helix: 0.38 (0.49), residues: 117 sheet: 1.03 (0.71), residues: 59 loop : -1.81 (0.47), 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 0.009 0.001 PHE K 784 TYR 0.014 0.002 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 54 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 470 LYS cc_start: 0.2969 (tmtt) cc_final: 0.2544 (mmmt) REVERT: K 572 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6153 (mt) REVERT: K 616 ARG cc_start: 0.8172 (mtp-110) cc_final: 0.7867 (mtm110) REVERT: K 672 LYS cc_start: 0.5831 (tppt) cc_final: 0.4712 (ptpt) REVERT: K 745 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5964 (mm) outliers start: 14 outliers final: 8 residues processed: 49 average time/residue: 0.1528 time to fit residues: 9.0744 Evaluate side-chains 50 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 604 GLU Chi-restraints excluded: chain K residue 629 LEU Chi-restraints excluded: chain K residue 669 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.0170 chunk 8 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 563 HIS K 746 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.214626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.189137 restraints weight = 3648.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.190712 restraints weight = 2831.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.192654 restraints weight = 1859.756| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2730 Z= 0.223 Angle : 0.642 9.473 3683 Z= 0.321 Chirality : 0.045 0.135 410 Planarity : 0.004 0.035 468 Dihedral : 4.668 15.226 354 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.33 % Allowed : 26.00 % 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: -0.80 (0.46), residues: 329 helix: 0.29 (0.49), residues: 117 sheet: 1.04 (0.70), residues: 59 loop : -1.90 (0.47), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP K 577 HIS 0.006 0.001 HIS K 651 PHE 0.009 0.001 PHE K 784 TYR 0.013 0.002 TYR K 580 ARG 0.003 0.000 ARG K 590 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1450.26 seconds wall clock time: 26 minutes 5.65 seconds (1565.65 seconds total)