Starting phenix.real_space_refine on Sun Mar 10 16:45:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/03_2024/8drq_27681.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/03_2024/8drq_27681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/03_2024/8drq_27681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/03_2024/8drq_27681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/03_2024/8drq_27681.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/03_2024/8drq_27681.pdb" } resolution = 4.16 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= 0.001 sd= 0.045 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 8 5.16 5 C 2135 2.51 5 N 583 2.21 5 O 595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 473": "OE1" <-> "OE2" Residue "E TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 519": "OE1" <-> "OE2" Residue "E GLU 520": "OE1" <-> "OE2" Residue "E ASP 538": "OD1" <-> "OD2" Residue "E ASP 620": "OD1" <-> "OD2" Residue "E GLU 760": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3321 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3321 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 18, 'TRANS': 388} Time building chain proxies: 2.35, per 1000 atoms: 0.71 Number of scatterers: 3321 At special positions: 0 Unit cell: (75.456, 81.744, 78.6, 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 8 16.00 O 595 8.00 N 583 7.00 C 2135 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 603.1 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 31.4% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'E' and resid 402 through 411 Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 439 through 444 removed outlier: 3.790A pdb=" N PHE E 443 " --> pdb=" O PRO E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 removed outlier: 3.589A pdb=" N ILE E 465 " --> pdb=" O PRO E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 510 through 514 removed outlier: 4.056A pdb=" N TYR E 513 " --> pdb=" O LEU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 541 removed outlier: 3.702A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 removed outlier: 3.788A pdb=" N THR E 563 " --> pdb=" O PRO E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 638 removed outlier: 3.750A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 661 removed outlier: 3.525A pdb=" N LEU E 661 " --> pdb=" O ILE E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 684 removed outlier: 3.647A pdb=" N CYS E 684 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 707 removed outlier: 3.953A pdb=" N ILE E 704 " --> pdb=" O PRO E 701 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 707 " --> pdb=" O ILE E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 730 removed outlier: 3.629A pdb=" N PHE E 728 " --> pdb=" O PRO E 724 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS E 730 " --> pdb=" O GLU E 726 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 753 Processing helix chain 'E' and resid 771 through 776 removed outlier: 3.560A pdb=" N CYS E 776 " --> pdb=" O GLU E 772 " (cutoff:3.500A) Processing helix chain 'E' and resid 788 through 793 Processing helix chain 'E' and resid 795 through 808 Processing sheet with id=AA1, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.410A pdb=" N LEU E 428 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS E 452 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU E 474 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LYS E 501 " --> pdb=" O LEU E 474 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU E 476 " --> pdb=" O LYS E 501 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU E 498 " --> pdb=" O HIS E 522 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR E 524 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE E 500 " --> pdb=" O THR E 524 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 596 " --> pdb=" O GLU E 618 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP E 620 " --> pdb=" O LEU E 596 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU E 598 " --> pdb=" O ASP E 620 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 459 through 460 removed outlier: 6.483A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 666 through 668 removed outlier: 6.334A pdb=" N TYR E 689 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU E 690 " --> pdb=" O ALA E 714 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 159 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: 0.78 Time building geometry restraints manager: 1.32 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: 1098 1.34 - 1.46: 490 1.46 - 1.58: 1779 1.58 - 1.69: 1 1.69 - 1.81: 10 Bond restraints: 3378 Sorted by residual: bond pdb=" N PRO E 678 " pdb=" CD PRO E 678 " ideal model delta sigma weight residual 1.473 1.417 0.056 1.40e-02 5.10e+03 1.59e+01 bond pdb=" CB PRO E 678 " pdb=" CG PRO E 678 " ideal model delta sigma weight residual 1.492 1.614 -0.122 5.00e-02 4.00e+02 5.92e+00 bond pdb=" CB ASN E 712 " pdb=" CG ASN E 712 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.36e+00 bond pdb=" CG PRO E 678 " pdb=" CD PRO E 678 " ideal model delta sigma weight residual 1.503 1.460 0.043 3.40e-02 8.65e+02 1.57e+00 bond pdb=" N TYR E 534 " pdb=" CA TYR E 534 " ideal model delta sigma weight residual 1.459 1.471 -0.012 1.15e-02 7.56e+03 1.15e+00 ... (remaining 3373 not shown) Histogram of bond angle deviations from ideal: 100.70 - 107.36: 114 107.36 - 114.03: 1986 114.03 - 120.70: 1286 120.70 - 127.37: 1160 127.37 - 134.03: 34 Bond angle restraints: 4580 Sorted by residual: angle pdb=" CA MET E 590 " pdb=" CB MET E 590 " pdb=" CG MET E 590 " ideal model delta sigma weight residual 114.10 121.55 -7.45 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CB MET E 590 " pdb=" CG MET E 590 " pdb=" SD MET E 590 " ideal model delta sigma weight residual 112.70 122.86 -10.16 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C ASN E 712 " pdb=" CA ASN E 712 " pdb=" CB ASN E 712 " ideal model delta sigma weight residual 109.38 115.03 -5.65 1.80e+00 3.09e-01 9.85e+00 angle pdb=" N PRO E 678 " pdb=" CD PRO E 678 " pdb=" CG PRO E 678 " ideal model delta sigma weight residual 103.20 107.80 -4.60 1.50e+00 4.44e-01 9.42e+00 angle pdb=" C LEU E 603 " pdb=" N GLU E 604 " pdb=" CA GLU E 604 " ideal model delta sigma weight residual 121.54 127.28 -5.74 1.91e+00 2.74e-01 9.02e+00 ... (remaining 4575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 1759 15.43 - 30.85: 250 30.85 - 46.28: 67 46.28 - 61.70: 17 61.70 - 77.13: 1 Dihedral angle restraints: 2094 sinusoidal: 892 harmonic: 1202 Sorted by residual: dihedral pdb=" CA LEU E 468 " pdb=" C LEU E 468 " pdb=" N THR E 469 " pdb=" CA THR E 469 " ideal model delta harmonic sigma weight residual 180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ILE E 535 " pdb=" C ILE E 535 " pdb=" N VAL E 536 " pdb=" CA VAL E 536 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA THR E 662 " pdb=" C THR E 662 " pdb=" N ASN E 663 " pdb=" CA ASN E 663 " ideal model delta harmonic sigma weight residual -180.00 -160.50 -19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 2091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 316 0.036 - 0.071: 163 0.071 - 0.107: 53 0.107 - 0.143: 15 0.143 - 0.178: 2 Chirality restraints: 549 Sorted by residual: chirality pdb=" CB VAL E 786 " pdb=" CA VAL E 786 " pdb=" CG1 VAL E 786 " pdb=" CG2 VAL E 786 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA VAL E 786 " pdb=" N VAL E 786 " pdb=" C VAL E 786 " pdb=" CB VAL E 786 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA ILE E 654 " pdb=" N ILE E 654 " pdb=" C ILE E 654 " pdb=" CB ILE E 654 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 546 not shown) Planarity restraints: 578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 677 " -0.047 5.00e-02 4.00e+02 7.27e-02 8.45e+00 pdb=" N PRO E 678 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 678 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 678 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 490 " -0.007 2.00e-02 2.50e+03 1.84e-02 5.90e+00 pdb=" CG PHE E 490 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE E 490 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE E 490 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE E 490 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 490 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 490 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 746 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO E 747 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 747 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 747 " 0.026 5.00e-02 4.00e+02 ... (remaining 575 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 850 2.81 - 3.33: 3133 3.33 - 3.85: 5736 3.85 - 4.38: 7140 4.38 - 4.90: 11097 Nonbonded interactions: 27956 Sorted by model distance: nonbonded pdb=" O VAL E 591 " pdb=" ND2 ASN E 615 " model vdw 2.283 2.520 nonbonded pdb=" O LEU E 476 " pdb=" N LYS E 501 " model vdw 2.300 2.520 nonbonded pdb=" OH TYR E 689 " pdb=" OE1 GLN E 711 " model vdw 2.315 2.440 nonbonded pdb=" O GLN E 560 " pdb=" OG1 THR E 563 " model vdw 2.328 2.440 nonbonded pdb=" O LEU E 790 " pdb=" OG1 THR E 793 " model vdw 2.329 2.440 ... (remaining 27951 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 3.160 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: 14.550 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.690 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5765 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 : 0.004 0.122 3378 Z= 0.295 Angle : 0.891 10.159 4580 Z= 0.486 Chirality : 0.048 0.178 549 Planarity : 0.006 0.073 578 Dihedral : 15.597 77.126 1306 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 19.31 % Favored : 80.69 % 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: -3.30 (0.39), residues: 405 helix: -3.27 (0.37), residues: 114 sheet: -2.33 (0.78), residues: 54 loop : -1.55 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 475 HIS 0.011 0.002 HIS E 694 PHE 0.039 0.003 PHE E 490 TYR 0.012 0.002 TYR E 477 ARG 0.003 0.000 ARG E 545 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 419 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8130 (tpt-90) REVERT: E 458 ASP cc_start: 0.7150 (m-30) cc_final: 0.6770 (t0) REVERT: E 465 ILE cc_start: 0.9158 (tt) cc_final: 0.8907 (tt) REVERT: E 474 LEU cc_start: 0.8956 (tt) cc_final: 0.8426 (tt) REVERT: E 496 ARG cc_start: 0.8407 (mtt90) cc_final: 0.8046 (mpt180) REVERT: E 507 GLU cc_start: 0.6049 (mt-10) cc_final: 0.5197 (mt-10) REVERT: E 520 GLU cc_start: 0.8635 (tt0) cc_final: 0.8389 (tt0) REVERT: E 555 LEU cc_start: 0.7678 (tp) cc_final: 0.7448 (tp) REVERT: E 581 LEU cc_start: 0.7922 (mp) cc_final: 0.7232 (tt) REVERT: E 592 ASN cc_start: 0.8192 (m-40) cc_final: 0.7941 (m110) REVERT: E 650 HIS cc_start: 0.6995 (m-70) cc_final: 0.6632 (m-70) REVERT: E 723 LEU cc_start: 0.5309 (mt) cc_final: 0.4532 (tt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2422 time to fit residues: 38.8709 Evaluate side-chains 97 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 0.0050 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.0770 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.9756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 614 HIS E 711 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5822 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3378 Z= 0.218 Angle : 0.739 10.537 4580 Z= 0.354 Chirality : 0.047 0.190 549 Planarity : 0.006 0.059 578 Dihedral : 5.649 17.825 439 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 24.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % 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: -3.65 (0.37), residues: 405 helix: -2.94 (0.35), residues: 141 sheet: -2.35 (0.68), residues: 58 loop : -1.96 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP E 647 HIS 0.016 0.002 HIS E 499 PHE 0.015 0.002 PHE E 490 TYR 0.029 0.004 TYR E 668 ARG 0.009 0.001 ARG E 666 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 443 PHE cc_start: 0.8120 (m-80) cc_final: 0.7792 (m-80) REVERT: E 496 ARG cc_start: 0.8192 (mtt90) cc_final: 0.7824 (mpt-90) REVERT: E 507 GLU cc_start: 0.6220 (mt-10) cc_final: 0.5882 (mt-10) REVERT: E 521 LEU cc_start: 0.8466 (tt) cc_final: 0.8082 (mt) REVERT: E 592 ASN cc_start: 0.8188 (m-40) cc_final: 0.7902 (m110) REVERT: E 601 CYS cc_start: 0.8085 (t) cc_final: 0.7819 (t) REVERT: E 603 LEU cc_start: 0.8187 (mt) cc_final: 0.7789 (mt) REVERT: E 640 ARG cc_start: 0.5978 (mpp-170) cc_final: 0.4485 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.2159 time to fit residues: 27.3701 Evaluate side-chains 82 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 0.0670 chunk 39 optimal weight: 0.0970 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 694 HIS E 741 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5869 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3378 Z= 0.177 Angle : 0.649 7.976 4580 Z= 0.312 Chirality : 0.044 0.176 549 Planarity : 0.005 0.057 578 Dihedral : 5.070 16.846 439 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: -3.10 (0.40), residues: 405 helix: -2.55 (0.41), residues: 128 sheet: -1.18 (0.85), residues: 43 loop : -1.95 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 647 HIS 0.008 0.002 HIS E 499 PHE 0.012 0.002 PHE E 490 TYR 0.015 0.002 TYR E 477 ARG 0.004 0.001 ARG E 666 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 443 PHE cc_start: 0.8100 (m-80) cc_final: 0.7798 (m-80) REVERT: E 454 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7788 (tm-30) REVERT: E 496 ARG cc_start: 0.8310 (mtt90) cc_final: 0.7844 (mpp80) REVERT: E 507 GLU cc_start: 0.6017 (mt-10) cc_final: 0.5783 (mt-10) REVERT: E 521 LEU cc_start: 0.8550 (tt) cc_final: 0.7925 (mt) REVERT: E 543 LEU cc_start: 0.7939 (mt) cc_final: 0.7718 (tp) REVERT: E 592 ASN cc_start: 0.8112 (m-40) cc_final: 0.7833 (m110) REVERT: E 640 ARG cc_start: 0.5753 (mpp-170) cc_final: 0.4174 (mmp-170) REVERT: E 685 ARG cc_start: 0.6856 (mmp-170) cc_final: 0.6156 (tpt-90) REVERT: E 732 LYS cc_start: 0.6819 (tptp) cc_final: 0.5771 (mptt) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1940 time to fit residues: 23.8174 Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 0.0980 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.0070 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 694 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5891 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3378 Z= 0.170 Angle : 0.638 7.798 4580 Z= 0.307 Chirality : 0.045 0.170 549 Planarity : 0.005 0.060 578 Dihedral : 4.856 15.018 439 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.26 % Allowed : 3.70 % Favored : 96.03 % 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: -3.07 (0.39), residues: 405 helix: -2.50 (0.41), residues: 131 sheet: -1.42 (0.77), residues: 48 loop : -1.87 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP E 647 HIS 0.004 0.001 HIS E 522 PHE 0.012 0.001 PHE E 490 TYR 0.013 0.002 TYR E 689 ARG 0.003 0.001 ARG E 545 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 443 PHE cc_start: 0.8071 (m-80) cc_final: 0.7766 (m-80) REVERT: E 496 ARG cc_start: 0.8446 (mtt90) cc_final: 0.8029 (mpp80) REVERT: E 507 GLU cc_start: 0.6318 (mt-10) cc_final: 0.6058 (mt-10) REVERT: E 520 GLU cc_start: 0.7891 (pt0) cc_final: 0.7591 (pp20) REVERT: E 521 LEU cc_start: 0.8455 (tt) cc_final: 0.7626 (mt) REVERT: E 592 ASN cc_start: 0.8144 (m-40) cc_final: 0.7820 (m110) REVERT: E 597 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7640 (tp30) REVERT: E 603 LEU cc_start: 0.7670 (mm) cc_final: 0.7358 (mm) REVERT: E 640 ARG cc_start: 0.5145 (mpp-170) cc_final: 0.3788 (mmp-170) REVERT: E 685 ARG cc_start: 0.6896 (mmp-170) cc_final: 0.6126 (tpt-90) REVERT: E 732 LYS cc_start: 0.6601 (tptp) cc_final: 0.5864 (mptt) outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.1961 time to fit residues: 21.3161 Evaluate side-chains 70 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3378 Z= 0.205 Angle : 0.653 7.959 4580 Z= 0.317 Chirality : 0.045 0.158 549 Planarity : 0.005 0.057 578 Dihedral : 4.939 15.301 439 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: -3.08 (0.39), residues: 405 helix: -2.44 (0.42), residues: 129 sheet: -1.16 (0.84), residues: 43 loop : -2.00 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP E 647 HIS 0.007 0.001 HIS E 522 PHE 0.013 0.002 PHE E 728 TYR 0.010 0.002 TYR E 668 ARG 0.011 0.001 ARG E 545 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 434 MET cc_start: 0.6820 (mmp) cc_final: 0.6578 (mmp) REVERT: E 475 TRP cc_start: 0.8576 (m-10) cc_final: 0.8374 (m-10) REVERT: E 496 ARG cc_start: 0.8472 (mtt90) cc_final: 0.8028 (mpp80) REVERT: E 521 LEU cc_start: 0.8597 (tt) cc_final: 0.8091 (mt) REVERT: E 592 ASN cc_start: 0.8116 (m-40) cc_final: 0.7832 (m110) REVERT: E 640 ARG cc_start: 0.5156 (mpp-170) cc_final: 0.3754 (mmp-170) REVERT: E 674 ILE cc_start: 0.7523 (pt) cc_final: 0.7261 (tp) REVERT: E 685 ARG cc_start: 0.6765 (mmp-170) cc_final: 0.6029 (tpt170) REVERT: E 729 GLN cc_start: 0.4563 (mp10) cc_final: 0.3183 (tt0) REVERT: E 732 LYS cc_start: 0.6885 (tptp) cc_final: 0.6141 (mptt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1802 time to fit residues: 18.6988 Evaluate side-chains 68 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 37 optimal weight: 0.0570 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.7061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3378 Z= 0.184 Angle : 0.658 7.977 4580 Z= 0.317 Chirality : 0.046 0.190 549 Planarity : 0.006 0.084 578 Dihedral : 5.006 15.139 439 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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: -2.97 (0.39), residues: 405 helix: -2.27 (0.44), residues: 125 sheet: -1.41 (0.74), residues: 48 loop : -1.92 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP E 647 HIS 0.004 0.001 HIS E 499 PHE 0.012 0.002 PHE E 490 TYR 0.016 0.002 TYR E 648 ARG 0.009 0.001 ARG E 545 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 475 TRP cc_start: 0.8303 (m-10) cc_final: 0.8033 (m-10) REVERT: E 496 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8168 (mmt90) REVERT: E 521 LEU cc_start: 0.8550 (tt) cc_final: 0.8008 (mt) REVERT: E 592 ASN cc_start: 0.8106 (m-40) cc_final: 0.7813 (m110) REVERT: E 640 ARG cc_start: 0.5286 (mpp-170) cc_final: 0.3878 (mmp-170) REVERT: E 670 ASN cc_start: 0.7418 (p0) cc_final: 0.7165 (p0) REVERT: E 674 ILE cc_start: 0.7526 (pt) cc_final: 0.7245 (tp) REVERT: E 729 GLN cc_start: 0.4470 (mp10) cc_final: 0.2982 (tt0) REVERT: E 732 LYS cc_start: 0.7137 (tptp) cc_final: 0.6417 (mptt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1684 time to fit residues: 16.3360 Evaluate side-chains 68 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 moved from start: 0.7534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3378 Z= 0.199 Angle : 0.699 7.624 4580 Z= 0.335 Chirality : 0.046 0.189 549 Planarity : 0.006 0.093 578 Dihedral : 5.146 22.364 439 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 23.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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: -3.09 (0.39), residues: 405 helix: -2.29 (0.43), residues: 125 sheet: -1.45 (0.77), residues: 43 loop : -2.06 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 647 HIS 0.004 0.001 HIS E 522 PHE 0.011 0.002 PHE E 490 TYR 0.023 0.002 TYR E 668 ARG 0.008 0.001 ARG E 545 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 475 TRP cc_start: 0.8417 (m-10) cc_final: 0.8015 (m-10) REVERT: E 496 ARG cc_start: 0.8623 (mtt90) cc_final: 0.8247 (mmt90) REVERT: E 521 LEU cc_start: 0.8610 (tt) cc_final: 0.8026 (mt) REVERT: E 532 ASN cc_start: 0.5801 (m-40) cc_final: 0.5397 (m-40) REVERT: E 592 ASN cc_start: 0.8183 (m-40) cc_final: 0.7854 (m110) REVERT: E 640 ARG cc_start: 0.5251 (mpp-170) cc_final: 0.3720 (mmp-170) REVERT: E 670 ASN cc_start: 0.7519 (p0) cc_final: 0.7301 (p0) REVERT: E 674 ILE cc_start: 0.7615 (pt) cc_final: 0.7328 (tp) REVERT: E 729 GLN cc_start: 0.4851 (mp10) cc_final: 0.4588 (pm20) REVERT: E 732 LYS cc_start: 0.7223 (tptp) cc_final: 0.6592 (mptt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1713 time to fit residues: 16.8055 Evaluate side-chains 68 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.7805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3378 Z= 0.179 Angle : 0.680 9.771 4580 Z= 0.321 Chirality : 0.045 0.169 549 Planarity : 0.005 0.066 578 Dihedral : 4.829 19.118 439 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.08 (0.38), residues: 405 helix: -2.31 (0.43), residues: 131 sheet: -1.34 (0.75), residues: 43 loop : -2.04 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP E 647 HIS 0.003 0.001 HIS E 522 PHE 0.015 0.002 PHE E 635 TYR 0.008 0.001 TYR E 689 ARG 0.009 0.000 ARG E 545 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 451 LEU cc_start: 0.8847 (tt) cc_final: 0.8578 (tt) REVERT: E 475 TRP cc_start: 0.8481 (m-10) cc_final: 0.8077 (m-10) REVERT: E 476 LEU cc_start: 0.8925 (mt) cc_final: 0.8700 (mp) REVERT: E 521 LEU cc_start: 0.8669 (tt) cc_final: 0.8407 (mt) REVERT: E 532 ASN cc_start: 0.5857 (m-40) cc_final: 0.5429 (m-40) REVERT: E 592 ASN cc_start: 0.8131 (m-40) cc_final: 0.7760 (m110) REVERT: E 640 ARG cc_start: 0.5365 (mpp-170) cc_final: 0.3912 (mmp-170) REVERT: E 670 ASN cc_start: 0.7402 (p0) cc_final: 0.7119 (p0) REVERT: E 674 ILE cc_start: 0.7571 (pt) cc_final: 0.7174 (tp) REVERT: E 732 LYS cc_start: 0.7150 (tptp) cc_final: 0.6614 (mptt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1491 time to fit residues: 15.5632 Evaluate side-chains 69 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 0.0070 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.8388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3378 Z= 0.238 Angle : 0.748 10.282 4580 Z= 0.353 Chirality : 0.048 0.180 549 Planarity : 0.005 0.064 578 Dihedral : 5.249 25.235 439 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 24.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: -3.12 (0.38), residues: 405 helix: -2.35 (0.43), residues: 125 sheet: -1.27 (0.78), residues: 43 loop : -2.10 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 647 HIS 0.003 0.001 HIS E 431 PHE 0.014 0.002 PHE E 443 TYR 0.023 0.002 TYR E 668 ARG 0.008 0.001 ARG E 545 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 475 TRP cc_start: 0.8420 (m-10) cc_final: 0.7682 (m-10) REVERT: E 496 ARG cc_start: 0.8513 (mpt-90) cc_final: 0.8061 (mpp80) REVERT: E 521 LEU cc_start: 0.8713 (tt) cc_final: 0.8355 (mt) REVERT: E 532 ASN cc_start: 0.6224 (m-40) cc_final: 0.5697 (m-40) REVERT: E 555 LEU cc_start: 0.7009 (tp) cc_final: 0.6775 (tp) REVERT: E 592 ASN cc_start: 0.8208 (m-40) cc_final: 0.7765 (m110) REVERT: E 670 ASN cc_start: 0.7427 (p0) cc_final: 0.7201 (p0) REVERT: E 674 ILE cc_start: 0.7678 (pt) cc_final: 0.7312 (tp) REVERT: E 729 GLN cc_start: 0.4679 (mp10) cc_final: 0.3166 (tt0) REVERT: E 732 LYS cc_start: 0.7060 (tptp) cc_final: 0.6648 (mptt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1540 time to fit residues: 15.4302 Evaluate side-chains 62 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.8629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3378 Z= 0.193 Angle : 0.702 10.698 4580 Z= 0.330 Chirality : 0.046 0.161 549 Planarity : 0.005 0.061 578 Dihedral : 5.031 22.157 439 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -3.02 (0.39), residues: 405 helix: -2.26 (0.44), residues: 125 sheet: -1.07 (0.80), residues: 43 loop : -2.08 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 647 HIS 0.005 0.001 HIS E 431 PHE 0.021 0.002 PHE E 443 TYR 0.008 0.001 TYR E 689 ARG 0.006 0.001 ARG E 640 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 409 ASN cc_start: 0.7724 (t0) cc_final: 0.7462 (t0) REVERT: E 475 TRP cc_start: 0.8531 (m-10) cc_final: 0.7978 (m-10) REVERT: E 484 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6222 (tt0) REVERT: E 496 ARG cc_start: 0.8527 (mpt-90) cc_final: 0.8004 (mpp80) REVERT: E 517 THR cc_start: 0.8615 (p) cc_final: 0.8414 (p) REVERT: E 521 LEU cc_start: 0.8760 (tt) cc_final: 0.8466 (mt) REVERT: E 532 ASN cc_start: 0.6099 (m-40) cc_final: 0.5582 (m-40) REVERT: E 555 LEU cc_start: 0.6869 (tp) cc_final: 0.6644 (tp) REVERT: E 592 ASN cc_start: 0.8141 (m-40) cc_final: 0.7669 (m110) REVERT: E 640 ARG cc_start: 0.4828 (mpp-170) cc_final: 0.3076 (tpp-160) REVERT: E 670 ASN cc_start: 0.7361 (p0) cc_final: 0.7098 (p0) REVERT: E 674 ILE cc_start: 0.7695 (pt) cc_final: 0.7345 (tp) REVERT: E 729 GLN cc_start: 0.4858 (mp10) cc_final: 0.3430 (tt0) REVERT: E 732 LYS cc_start: 0.7036 (tptp) cc_final: 0.6648 (mptt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1486 time to fit residues: 15.7953 Evaluate side-chains 74 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 39 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.135964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.122589 restraints weight = 15597.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.124179 restraints weight = 11883.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.125457 restraints weight = 9265.416| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.8908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3378 Z= 0.210 Angle : 0.726 10.175 4580 Z= 0.343 Chirality : 0.047 0.200 549 Planarity : 0.005 0.060 578 Dihedral : 5.156 25.007 439 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.83 (0.40), residues: 405 helix: -2.33 (0.45), residues: 119 sheet: -0.80 (0.82), residues: 43 loop : -1.89 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 647 HIS 0.002 0.001 HIS E 694 PHE 0.016 0.002 PHE E 443 TYR 0.026 0.003 TYR E 668 ARG 0.010 0.001 ARG E 545 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1476.34 seconds wall clock time: 27 minutes 6.85 seconds (1626.85 seconds total)