Starting phenix.real_space_refine on Sat Aug 3 05:55:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r35_18861/08_2024/8r35_18861.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r35_18861/08_2024/8r35_18861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r35_18861/08_2024/8r35_18861.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r35_18861/08_2024/8r35_18861.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r35_18861/08_2024/8r35_18861.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r35_18861/08_2024/8r35_18861.cif" } resolution = 3.12 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= 0.005 sd= 0.038 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 52 5.16 5 C 4755 2.51 5 N 1112 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B GLU 492": "OE1" <-> "OE2" Residue "B ASP 575": "OD1" <-> "OD2" Residue "B GLU 684": "OE1" <-> "OE2" Residue "B ASP 795": "OD1" <-> "OD2" Residue "B PHE 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 839": "OD1" <-> "OD2" Residue "B TYR 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7150 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3530 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain: "B" Number of atoms: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3620 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain breaks: 1 Time building chain proxies: 5.74, per 1000 atoms: 0.80 Number of scatterers: 7150 At special positions: 0 Unit cell: (83.085, 86.523, 100.275, 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 52 16.00 O 1231 8.00 N 1112 7.00 C 4755 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: 2.97 Conformation dependent library (CDL) restraints added in 1.2 seconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 411 through 430 Processing helix chain 'A' and resid 435 through 455 Processing helix chain 'A' and resid 458 through 474 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 485 through 498 removed outlier: 3.508A pdb=" N MET A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TRP A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 518 removed outlier: 3.663A pdb=" N MET A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 533 removed outlier: 3.631A pdb=" N LEU A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 567 removed outlier: 3.622A pdb=" N LEU A 540 " --> pdb=" O PRO A 536 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TRP A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ASN A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N VAL A 557 " --> pdb=" O TRP A 553 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ALA A 558 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Proline residue: A 560 - end of helix Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 578 through 596 Processing helix chain 'A' and resid 603 through 614 Processing helix chain 'A' and resid 619 through 646 removed outlier: 3.612A pdb=" N PHE A 624 " --> pdb=" O TRP A 620 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 626 " --> pdb=" O GLN A 622 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 664 through 683 Processing helix chain 'A' and resid 684 through 686 No H-bonds generated for 'chain 'A' and resid 684 through 686' Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.561A pdb=" N ILE A 697 " --> pdb=" O SER A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.518A pdb=" N PHE A 705 " --> pdb=" O PRO A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 removed outlier: 3.624A pdb=" N LEU A 716 " --> pdb=" O SER A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 741 removed outlier: 3.926A pdb=" N VAL A 724 " --> pdb=" O PRO A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 754 Processing helix chain 'A' and resid 758 through 777 removed outlier: 4.044A pdb=" N PHE A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 797 Proline residue: A 788 - end of helix Processing helix chain 'A' and resid 801 through 814 Processing helix chain 'A' and resid 824 through 832 Processing helix chain 'A' and resid 843 through 874 Proline residue: A 853 - end of helix removed outlier: 4.644A pdb=" N TYR A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 411 through 430 Processing helix chain 'B' and resid 435 through 455 Processing helix chain 'B' and resid 458 through 474 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 485 through 496 Processing helix chain 'B' and resid 499 through 518 removed outlier: 3.515A pdb=" N MET B 503 " --> pdb=" O SER B 499 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 533 removed outlier: 4.133A pdb=" N LEU B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.983A pdb=" N MET B 552 " --> pdb=" O PHE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 567 removed outlier: 4.153A pdb=" N ALA B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) Proline residue: B 560 - end of helix Processing helix chain 'B' and resid 567 through 574 Processing helix chain 'B' and resid 584 through 586 No H-bonds generated for 'chain 'B' and resid 584 through 586' Processing helix chain 'B' and resid 587 through 594 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 603 through 614 removed outlier: 3.939A pdb=" N SER B 611 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR B 612 " --> pdb=" O ILE B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 617 No H-bonds generated for 'chain 'B' and resid 615 through 617' Processing helix chain 'B' and resid 619 through 626 Processing helix chain 'B' and resid 626 through 647 removed outlier: 3.876A pdb=" N SER B 630 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS B 647 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 683 Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 693 through 698 Processing helix chain 'B' and resid 698 through 707 removed outlier: 3.946A pdb=" N ILE B 702 " --> pdb=" O ALA B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 719 removed outlier: 3.590A pdb=" N LEU B 716 " --> pdb=" O SER B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 741 removed outlier: 4.051A pdb=" N VAL B 724 " --> pdb=" O PRO B 720 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 741 " --> pdb=" O VAL B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 754 Processing helix chain 'B' and resid 758 through 777 removed outlier: 3.646A pdb=" N LEU B 769 " --> pdb=" O ILE B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 797 removed outlier: 3.751A pdb=" N ILE B 787 " --> pdb=" O ALA B 783 " (cutoff:3.500A) Proline residue: B 788 - end of helix Processing helix chain 'B' and resid 801 through 815 removed outlier: 4.293A pdb=" N SER B 815 " --> pdb=" O ALA B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 832 Processing helix chain 'B' and resid 843 through 864 removed outlier: 4.567A pdb=" N VAL B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Proline residue: B 853 - end of helix Processing helix chain 'B' and resid 864 through 874 503 hydrogen bonds defined for protein. 1500 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: 2.07 Time building geometry restraints manager: 3.15 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: 2117 1.34 - 1.46: 1625 1.46 - 1.58: 3473 1.58 - 1.69: 1 1.69 - 1.81: 86 Bond restraints: 7302 Sorted by residual: bond pdb=" N VAL A 423 " pdb=" CA VAL A 423 " ideal model delta sigma weight residual 1.461 1.495 -0.033 1.17e-02 7.31e+03 8.14e+00 bond pdb=" N ILE A 417 " pdb=" CA ILE A 417 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.88e+00 bond pdb=" N ILE A 421 " pdb=" CA ILE A 421 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.57e+00 bond pdb=" N ILE A 420 " pdb=" CA ILE A 420 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.35e+00 bond pdb=" N THR A 424 " pdb=" CA THR A 424 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.12e+00 ... (remaining 7297 not shown) Histogram of bond angle deviations from ideal: 98.99 - 105.99: 175 105.99 - 112.99: 4112 112.99 - 119.99: 2443 119.99 - 126.99: 3117 126.99 - 133.99: 79 Bond angle restraints: 9926 Sorted by residual: angle pdb=" CA PRO B 800 " pdb=" N PRO B 800 " pdb=" CD PRO B 800 " ideal model delta sigma weight residual 112.00 105.52 6.48 1.40e+00 5.10e-01 2.14e+01 angle pdb=" CA MET B 635 " pdb=" CB MET B 635 " pdb=" CG MET B 635 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" N LEU A 426 " pdb=" CA LEU A 426 " pdb=" C LEU A 426 " ideal model delta sigma weight residual 111.07 107.67 3.40 1.07e+00 8.73e-01 1.01e+01 angle pdb=" C ILE B 863 " pdb=" N THR B 864 " pdb=" CA THR B 864 " ideal model delta sigma weight residual 122.56 117.83 4.73 1.50e+00 4.44e-01 9.94e+00 angle pdb=" N ILE B 601 " pdb=" CA ILE B 601 " pdb=" C ILE B 601 " ideal model delta sigma weight residual 111.91 109.13 2.78 8.90e-01 1.26e+00 9.79e+00 ... (remaining 9921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 3673 17.48 - 34.95: 499 34.95 - 52.43: 113 52.43 - 69.90: 15 69.90 - 87.38: 6 Dihedral angle restraints: 4306 sinusoidal: 1574 harmonic: 2732 Sorted by residual: dihedral pdb=" CA MET B 597 " pdb=" C MET B 597 " pdb=" N SER B 598 " pdb=" CA SER B 598 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CB GLU A 513 " pdb=" CG GLU A 513 " pdb=" CD GLU A 513 " pdb=" OE1 GLU A 513 " ideal model delta sinusoidal sigma weight residual 0.00 87.38 -87.38 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" N LYS B 752 " pdb=" CA LYS B 752 " pdb=" CB LYS B 752 " pdb=" CG LYS B 752 " ideal model delta sinusoidal sigma weight residual -60.00 -116.13 56.13 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 4303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 896 0.038 - 0.075: 248 0.075 - 0.113: 78 0.113 - 0.150: 5 0.150 - 0.188: 6 Chirality restraints: 1233 Sorted by residual: chirality pdb=" CA ILE A 421 " pdb=" N ILE A 421 " pdb=" C ILE A 421 " pdb=" CB ILE A 421 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA ILE A 420 " pdb=" N ILE A 420 " pdb=" C ILE A 420 " pdb=" CB ILE A 420 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA LEU A 426 " pdb=" N LEU A 426 " pdb=" C LEU A 426 " pdb=" CB LEU A 426 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 1230 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 799 " -0.060 5.00e-02 4.00e+02 8.72e-02 1.22e+01 pdb=" N PRO B 800 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 800 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 800 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 862 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C VAL B 862 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL B 862 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE B 863 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 603 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO B 604 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 604 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 604 " -0.022 5.00e-02 4.00e+02 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 955 2.75 - 3.29: 7375 3.29 - 3.83: 12290 3.83 - 4.36: 14118 4.36 - 4.90: 24727 Nonbonded interactions: 59465 Sorted by model distance: nonbonded pdb=" OE1 GLU B 684 " pdb=" OG SER B 694 " model vdw 2.214 3.040 nonbonded pdb=" O ASN B 593 " pdb=" OG SER B 815 " model vdw 2.226 3.040 nonbonded pdb=" O GLY B 595 " pdb=" OG SER B 602 " model vdw 2.245 3.040 nonbonded pdb=" O GLY A 707 " pdb=" NZ LYS B 413 " model vdw 2.269 3.120 nonbonded pdb=" O MET A 552 " pdb=" OG SER A 599 " model vdw 2.277 3.040 ... (remaining 59460 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 407 through 877) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.380 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 0.111 7302 Z= 0.197 Angle : 0.546 9.038 9926 Z= 0.305 Chirality : 0.039 0.188 1233 Planarity : 0.005 0.087 1185 Dihedral : 16.594 87.379 2546 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.90 % Allowed : 27.35 % Favored : 71.74 % 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: 1.44 (0.28), residues: 947 helix: 1.66 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.92 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 553 HIS 0.001 0.001 HIS B 460 PHE 0.014 0.001 PHE A 643 TYR 0.006 0.001 TYR B 867 ARG 0.004 0.000 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.799 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 91 average time/residue: 0.1560 time to fit residues: 20.4248 Evaluate side-chains 91 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 552 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 791 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7302 Z= 0.207 Angle : 0.514 5.841 9926 Z= 0.265 Chirality : 0.038 0.127 1233 Planarity : 0.004 0.045 1185 Dihedral : 4.074 48.990 987 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.45 % Allowed : 25.16 % Favored : 72.39 % 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: 1.77 (0.28), residues: 947 helix: 1.89 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.98 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 527 HIS 0.005 0.001 HIS B 439 PHE 0.016 0.001 PHE A 643 TYR 0.010 0.001 TYR B 518 ARG 0.003 0.000 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 0.835 Fit side-chains REVERT: B 446 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8706 (tm-30) REVERT: B 635 MET cc_start: 0.7724 (tmm) cc_final: 0.7440 (ttm) outliers start: 19 outliers final: 10 residues processed: 107 average time/residue: 0.1501 time to fit residues: 23.6137 Evaluate side-chains 95 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 769 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.8481 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7302 Z= 0.182 Angle : 0.507 6.511 9926 Z= 0.259 Chirality : 0.038 0.184 1233 Planarity : 0.004 0.047 1185 Dihedral : 3.801 36.866 985 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.10 % Allowed : 25.68 % Favored : 71.23 % 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: 1.89 (0.28), residues: 947 helix: 2.00 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.99 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 527 HIS 0.004 0.001 HIS B 439 PHE 0.016 0.001 PHE A 643 TYR 0.009 0.001 TYR B 518 ARG 0.009 0.001 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 801 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8083 (mtpt) REVERT: B 643 PHE cc_start: 0.7345 (t80) cc_final: 0.7118 (t80) outliers start: 24 outliers final: 11 residues processed: 104 average time/residue: 0.1686 time to fit residues: 25.0668 Evaluate side-chains 95 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 801 LYS Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 769 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.8480 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7302 Z= 0.181 Angle : 0.504 5.874 9926 Z= 0.257 Chirality : 0.038 0.189 1233 Planarity : 0.004 0.039 1185 Dihedral : 3.809 39.895 985 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.84 % Allowed : 25.42 % Favored : 71.74 % 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: 1.94 (0.28), residues: 947 helix: 2.02 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.93 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 527 HIS 0.004 0.001 HIS A 439 PHE 0.016 0.001 PHE A 643 TYR 0.009 0.001 TYR B 518 ARG 0.006 0.001 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 0.803 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 101 average time/residue: 0.1677 time to fit residues: 24.1381 Evaluate side-chains 96 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 769 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 78 optimal weight: 0.1980 chunk 63 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8456 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7302 Z= 0.148 Angle : 0.508 9.262 9926 Z= 0.255 Chirality : 0.038 0.199 1233 Planarity : 0.004 0.038 1185 Dihedral : 3.824 43.465 985 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.61 % Allowed : 24.52 % Favored : 71.87 % 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: 2.09 (0.28), residues: 947 helix: 2.13 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.92 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 527 HIS 0.004 0.001 HIS A 439 PHE 0.013 0.001 PHE A 643 TYR 0.007 0.001 TYR A 518 ARG 0.013 0.001 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: B 524 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8156 (mp) REVERT: B 635 MET cc_start: 0.7678 (tmm) cc_final: 0.7234 (ttm) outliers start: 28 outliers final: 17 residues processed: 106 average time/residue: 0.1532 time to fit residues: 23.3212 Evaluate side-chains 104 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 769 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 0.0370 chunk 82 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 76 optimal weight: 0.0570 chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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: 0.8437 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7302 Z= 0.143 Angle : 0.502 8.022 9926 Z= 0.253 Chirality : 0.038 0.213 1233 Planarity : 0.004 0.038 1185 Dihedral : 3.801 43.980 985 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.35 % Allowed : 24.00 % Favored : 72.65 % 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: 2.18 (0.28), residues: 947 helix: 2.22 (0.20), residues: 701 sheet: None (None), residues: 0 loop : -0.87 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 553 HIS 0.004 0.001 HIS A 439 PHE 0.011 0.001 PHE A 643 TYR 0.007 0.001 TYR B 518 ARG 0.010 0.001 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 0.816 Fit side-chains REVERT: B 464 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8607 (m-80) REVERT: B 524 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8161 (mp) REVERT: B 635 MET cc_start: 0.7651 (tmm) cc_final: 0.7443 (ttm) outliers start: 26 outliers final: 16 residues processed: 109 average time/residue: 0.1412 time to fit residues: 22.7180 Evaluate side-chains 103 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 769 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8467 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7302 Z= 0.180 Angle : 0.517 8.974 9926 Z= 0.259 Chirality : 0.038 0.129 1233 Planarity : 0.004 0.039 1185 Dihedral : 3.834 45.882 985 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.13 % Allowed : 23.61 % Favored : 72.26 % 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: 2.18 (0.28), residues: 947 helix: 2.19 (0.20), residues: 707 sheet: None (None), residues: 0 loop : -0.87 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 553 HIS 0.009 0.002 HIS A 439 PHE 0.015 0.001 PHE A 643 TYR 0.009 0.001 TYR A 518 ARG 0.007 0.001 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 87 time to evaluate : 0.809 Fit side-chains REVERT: B 464 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8629 (m-80) REVERT: B 524 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8180 (mp) outliers start: 32 outliers final: 23 residues processed: 108 average time/residue: 0.1409 time to fit residues: 22.6193 Evaluate side-chains 111 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 86 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 769 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 0.0870 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 0.0770 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6316 ------------------------------------------------------------------------------- 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: 0.8446 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7302 Z= 0.153 Angle : 0.504 7.400 9926 Z= 0.254 Chirality : 0.037 0.128 1233 Planarity : 0.004 0.038 1185 Dihedral : 3.862 48.269 985 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.23 % Allowed : 24.52 % Favored : 72.26 % 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: 2.26 (0.28), residues: 947 helix: 2.27 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.90 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 553 HIS 0.009 0.002 HIS A 439 PHE 0.012 0.001 PHE A 643 TYR 0.008 0.001 TYR B 518 ARG 0.006 0.000 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 0.792 Fit side-chains REVERT: B 464 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8597 (m-80) REVERT: B 524 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8147 (mp) outliers start: 25 outliers final: 21 residues processed: 101 average time/residue: 0.1400 time to fit residues: 20.9498 Evaluate side-chains 107 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 870 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 80 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.8446 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7302 Z= 0.155 Angle : 0.511 7.109 9926 Z= 0.256 Chirality : 0.037 0.128 1233 Planarity : 0.004 0.038 1185 Dihedral : 3.854 48.539 985 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.61 % Allowed : 24.26 % Favored : 72.13 % 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: 2.29 (0.28), residues: 947 helix: 2.28 (0.20), residues: 707 sheet: None (None), residues: 0 loop : -0.87 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 553 HIS 0.008 0.002 HIS A 439 PHE 0.013 0.001 PHE A 643 TYR 0.008 0.001 TYR B 518 ARG 0.006 0.000 ARG B 840 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 86 time to evaluate : 0.815 Fit side-chains REVERT: B 464 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8521 (m-80) REVERT: B 524 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8152 (mp) REVERT: B 635 MET cc_start: 0.7584 (tmm) cc_final: 0.6794 (ttm) outliers start: 28 outliers final: 20 residues processed: 104 average time/residue: 0.1395 time to fit residues: 21.6134 Evaluate side-chains 107 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 769 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.0030 chunk 62 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 7 optimal weight: 0.0050 chunk 58 optimal weight: 0.0270 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 overall best weight: 0.3062 ------------------------------------------------------------------------------- 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: 0.8410 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7302 Z= 0.139 Angle : 0.530 10.134 9926 Z= 0.261 Chirality : 0.038 0.241 1233 Planarity : 0.004 0.037 1185 Dihedral : 3.840 50.264 985 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.71 % Allowed : 25.42 % Favored : 71.87 % 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: 2.35 (0.28), residues: 947 helix: 2.35 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.91 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 553 HIS 0.008 0.001 HIS A 439 PHE 0.009 0.001 PHE A 643 TYR 0.006 0.001 TYR B 518 ARG 0.006 0.000 ARG B 840 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.794 Fit side-chains REVERT: B 464 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8511 (m-10) REVERT: B 524 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8140 (mp) REVERT: B 635 MET cc_start: 0.7552 (tmm) cc_final: 0.7044 (ttm) outliers start: 21 outliers final: 17 residues processed: 102 average time/residue: 0.1426 time to fit residues: 21.5264 Evaluate side-chains 104 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 847 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 769 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 54 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.129696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.105624 restraints weight = 10950.537| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.73 r_work: 0.3300 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7302 Z= 0.152 Angle : 0.525 8.975 9926 Z= 0.260 Chirality : 0.038 0.276 1233 Planarity : 0.004 0.037 1185 Dihedral : 3.832 51.430 985 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.71 % Allowed : 25.29 % Favored : 72.00 % 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: 2.40 (0.28), residues: 947 helix: 2.36 (0.20), residues: 707 sheet: None (None), residues: 0 loop : -0.83 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 553 HIS 0.008 0.002 HIS A 439 PHE 0.012 0.001 PHE A 643 TYR 0.008 0.001 TYR B 518 ARG 0.006 0.000 ARG B 840 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1894.84 seconds wall clock time: 34 minutes 28.28 seconds (2068.28 seconds total)