Starting phenix.real_space_refine (version: dev) on Wed Apr 6 14:48:27 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/04_2022/7lyc_23592.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/04_2022/7lyc_23592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/04_2022/7lyc_23592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/04_2022/7lyc_23592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/04_2022/7lyc_23592.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyc_23592/04_2022/7lyc_23592.pdb" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.072 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 15475 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "H" Number of atoms: 737 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 735 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 639 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "N" Number of atoms: 2683 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 335, 2663 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 335, 2663 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain breaks: 1 bond proxies already assigned to first conformer: 2702 Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU K 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU K 73 " occ=0.45 residue: pdb=" N ASER N 452 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER N 452 " occ=0.50 Time building chain proxies: 9.83, per 1000 atoms: 0.64 Number of scatterers: 15475 At special positions: 0 Unit cell: (108.926, 117.146, 118.174, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 293 15.00 O 3445 8.00 N 2874 7.00 C 8834 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: 8.00 Conformation dependent library (CDL) restraints added in 2.2 seconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 61.7% alpha, 5.8% beta 140 base pairs and 263 stacking pairs defined. Time for finding SS restraints: 7.42 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.677A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.520A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.661A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.505A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 56 through 60 Processing helix chain 'N' and resid 430 through 439 Processing helix chain 'N' and resid 440 through 450 Processing helix chain 'N' and resid 463 through 472 Processing helix chain 'N' and resid 473 through 483 Processing helix chain 'N' and resid 491 through 495 Processing helix chain 'N' and resid 496 through 505 Processing helix chain 'N' and resid 506 through 516 Processing helix chain 'N' and resid 529 through 534 Processing helix chain 'N' and resid 536 through 544 Processing helix chain 'N' and resid 578 through 593 Processing helix chain 'N' and resid 617 through 626 Processing helix chain 'N' and resid 633 through 643 removed outlier: 3.554A pdb=" N LYS N 637 " --> pdb=" O PHE N 633 " (cutoff:3.500A) Processing helix chain 'N' and resid 648 through 652 removed outlier: 3.804A pdb=" N GLU N 652 " --> pdb=" O GLU N 649 " (cutoff:3.500A) Processing helix chain 'N' and resid 656 through 666 removed outlier: 3.915A pdb=" N SER N 660 " --> pdb=" O GLY N 656 " (cutoff:3.500A) Processing helix chain 'N' and resid 687 through 698 Processing helix chain 'N' and resid 711 through 716 Processing helix chain 'N' and resid 760 through 770 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.527A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.943A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.369A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.085A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.951A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.399A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.104A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'K' and resid 12 through 17 removed outlier: 9.097A pdb=" N LEU K 67 " --> pdb=" O GLN K 2 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE K 4 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU K 69 " --> pdb=" O PHE K 4 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS K 6 " --> pdb=" O LEU K 69 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N LEU K 71 " --> pdb=" O LYS K 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 595 through 597 removed outlier: 4.380A pdb=" N GLY N 574 " --> pdb=" O TYR N 597 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL N 571 " --> pdb=" O HIS N 606 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL N 608 " --> pdb=" O VAL N 571 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE N 573 " --> pdb=" O VAL N 608 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 701 through 702 removed outlier: 6.455A pdb=" N TYR N 676 " --> pdb=" O TYR N 736 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE N 738 " --> pdb=" O TYR N 676 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR N 678 " --> pdb=" O ILE N 738 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN N 735 " --> pdb=" O TRP N 756 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA N 758 " --> pdb=" O GLN N 735 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE N 737 " --> pdb=" O ALA N 758 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1559 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 358 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 263 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 8.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1965 1.32 - 1.44: 5712 1.44 - 1.56: 8057 1.56 - 1.69: 584 1.69 - 1.81: 45 Bond restraints: 16363 Sorted by residual: bond pdb=" C GLU E 50 " pdb=" O GLU E 50 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.19e-02 7.06e+03 1.00e+01 bond pdb=" C ARG E 116 " pdb=" O ARG E 116 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.28e-02 6.10e+03 9.86e+00 bond pdb=" C LYS D 116 " pdb=" O LYS D 116 " ideal model delta sigma weight residual 1.237 1.200 0.036 1.19e-02 7.06e+03 9.24e+00 bond pdb=" C VAL E 117 " pdb=" O VAL E 117 " ideal model delta sigma weight residual 1.236 1.203 0.034 1.19e-02 7.06e+03 7.95e+00 bond pdb=" C GLN A 76 " pdb=" N ASP A 77 " ideal model delta sigma weight residual 1.335 1.301 0.034 1.34e-02 5.57e+03 6.47e+00 ... (remaining 16358 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.58: 1490 105.58 - 112.68: 9082 112.68 - 119.78: 5371 119.78 - 126.88: 6595 126.88 - 133.98: 822 Bond angle restraints: 23360 Sorted by residual: angle pdb=" N ALA A 114 " pdb=" CA ALA A 114 " pdb=" C ALA A 114 " ideal model delta sigma weight residual 113.15 108.44 4.71 1.19e+00 7.06e-01 1.57e+01 angle pdb=" N GLU C 91 " pdb=" CA GLU C 91 " pdb=" C GLU C 91 " ideal model delta sigma weight residual 111.36 115.33 -3.97 1.09e+00 8.42e-01 1.33e+01 angle pdb=" N LEU E 48 " pdb=" CA LEU E 48 " pdb=" C LEU E 48 " ideal model delta sigma weight residual 111.36 107.58 3.78 1.09e+00 8.42e-01 1.20e+01 angle pdb=" N ARG A 116 " pdb=" CA ARG A 116 " pdb=" C ARG A 116 " ideal model delta sigma weight residual 109.41 104.69 4.72 1.52e+00 4.33e-01 9.64e+00 angle pdb=" N GLU A 50 " pdb=" CA GLU A 50 " pdb=" C GLU A 50 " ideal model delta sigma weight residual 111.28 114.41 -3.13 1.09e+00 8.42e-01 8.24e+00 ... (remaining 23355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.16: 7303 33.16 - 66.31: 1520 66.31 - 99.47: 38 99.47 - 132.62: 0 132.62 - 165.78: 2 Dihedral angle restraints: 8863 sinusoidal: 5411 harmonic: 3452 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual -180.00 -159.17 -20.83 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 54.22 165.78 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 66.57 153.43 1 3.50e+01 8.16e-04 1.48e+01 ... (remaining 8860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2311 0.062 - 0.123: 313 0.123 - 0.185: 20 0.185 - 0.247: 0 0.247 - 0.308: 1 Chirality restraints: 2645 Sorted by residual: chirality pdb=" CA GLN A 76 " pdb=" N GLN A 76 " pdb=" C GLN A 76 " pdb=" CB GLN A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA LEU N 625 " pdb=" N LEU N 625 " pdb=" C LEU N 625 " pdb=" CB LEU N 625 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA ILE N 573 " pdb=" N ILE N 573 " pdb=" C ILE N 573 " pdb=" CB ILE N 573 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 2642 not shown) Planarity restraints: 1948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -52 " 0.011 2.00e-02 2.50e+03 1.36e-02 5.57e+00 pdb=" N9 DG I -52 " -0.001 2.00e-02 2.50e+03 pdb=" C8 DG I -52 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I -52 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I -52 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DG I -52 " -0.016 2.00e-02 2.50e+03 pdb=" O6 DG I -52 " 0.018 2.00e-02 2.50e+03 pdb=" N1 DG I -52 " 0.009 2.00e-02 2.50e+03 pdb=" C2 DG I -52 " -0.033 2.00e-02 2.50e+03 pdb=" N2 DG I -52 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DG I -52 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DG I -52 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO D 103 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 496 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO N 497 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO N 497 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO N 497 " 0.028 5.00e-02 4.00e+02 ... (remaining 1945 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 3 2.03 - 2.75: 1847 2.75 - 3.47: 19710 3.47 - 4.18: 44026 4.18 - 4.90: 68237 Nonbonded interactions: 133823 Sorted by model distance: nonbonded pdb=" C SER H 123 " pdb=" N SER G 11 " model vdw 1.314 3.350 nonbonded pdb=" C SER D 123 " pdb=" N SER C 11 " model vdw 1.329 3.350 nonbonded pdb=" NH1 ARG N 427 " pdb=" OE1 GLU N 429 " model vdw 1.972 2.520 nonbonded pdb=" O ASN N 626 " pdb=" OD1 ASN N 626 " model vdw 2.086 3.040 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.179 2.496 ... (remaining 133818 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 20 through 102) selection = (chain 'F' and (resid 20 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 123)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 293 5.49 5 S 29 5.16 5 C 8834 2.51 5 N 2874 2.21 5 O 3445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 5.500 Check model and map are aligned: 0.250 Convert atoms to be neutral: 0.130 Process input model: 53.170 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 0.006 0.048 16363 Z= 0.349 Angle : 0.647 5.980 23360 Z= 0.396 Chirality : 0.042 0.308 2645 Planarity : 0.005 0.051 1948 Dihedral : 25.879 165.775 6639 Min Nonbonded Distance : 1.314 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.23), residues: 1172 helix: 0.47 (0.19), residues: 709 sheet: 0.08 (0.69), residues: 58 loop : -0.73 (0.28), residues: 405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.334 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 1.8791 time to fit residues: 295.8728 Evaluate side-chains 112 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 67 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 68 GLN B 75 HIS E 68 GLN E 76 GLN N 626 ASN C 104 GLN G 24 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 16363 Z= 0.223 Angle : 0.563 6.462 23360 Z= 0.334 Chirality : 0.037 0.187 2645 Planarity : 0.004 0.046 1948 Dihedral : 29.361 166.733 4261 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 1.18 % 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: 1.01 (0.24), residues: 1172 helix: 1.39 (0.19), residues: 718 sheet: 0.12 (0.69), residues: 58 loop : -0.49 (0.29), residues: 396 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.318 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 128 average time/residue: 1.8701 time to fit residues: 256.8520 Evaluate side-chains 120 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 1.301 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.1278 time to fit residues: 2.3710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 93 GLN N 470 ASN N 483 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 16363 Z= 0.308 Angle : 0.590 6.916 23360 Z= 0.346 Chirality : 0.039 0.175 2645 Planarity : 0.005 0.048 1948 Dihedral : 29.445 166.182 4261 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 2.07 % 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: 1.14 (0.24), residues: 1172 helix: 1.50 (0.19), residues: 719 sheet: 0.20 (0.72), residues: 53 loop : -0.46 (0.29), residues: 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.341 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 128 average time/residue: 1.8435 time to fit residues: 254.0121 Evaluate side-chains 121 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.311 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 5 average time/residue: 0.3650 time to fit residues: 4.0511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 483 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 16363 Z= 0.217 Angle : 0.567 6.975 23360 Z= 0.336 Chirality : 0.037 0.220 2645 Planarity : 0.004 0.047 1948 Dihedral : 29.438 166.481 4261 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 1.57 % 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: 1.31 (0.24), residues: 1172 helix: 1.65 (0.19), residues: 720 sheet: 0.24 (0.73), residues: 53 loop : -0.41 (0.29), residues: 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 1.456 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 122 average time/residue: 1.7206 time to fit residues: 226.3827 Evaluate side-chains 123 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.3494 time to fit residues: 3.9496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 483 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 16363 Z= 0.224 Angle : 0.559 8.663 23360 Z= 0.331 Chirality : 0.037 0.163 2645 Planarity : 0.004 0.047 1948 Dihedral : 29.400 167.364 4261 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 1.28 % 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: 1.37 (0.24), residues: 1172 helix: 1.69 (0.19), residues: 720 sheet: 0.30 (0.74), residues: 53 loop : -0.40 (0.29), residues: 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.254 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 123 average time/residue: 1.6244 time to fit residues: 216.5203 Evaluate side-chains 122 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.321 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.3536 time to fit residues: 4.0005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN N 483 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 16363 Z= 0.224 Angle : 0.544 7.650 23360 Z= 0.322 Chirality : 0.036 0.203 2645 Planarity : 0.004 0.047 1948 Dihedral : 29.269 168.895 4261 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 1.97 % 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: 1.53 (0.24), residues: 1172 helix: 1.81 (0.19), residues: 720 sheet: 0.39 (0.75), residues: 53 loop : -0.33 (0.30), residues: 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.342 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 121 average time/residue: 1.7012 time to fit residues: 222.3547 Evaluate side-chains 123 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.310 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.3548 time to fit residues: 4.0165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 82 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN N 483 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.065 16363 Z= 0.455 Angle : 0.649 8.869 23360 Z= 0.373 Chirality : 0.044 0.210 2645 Planarity : 0.005 0.052 1948 Dihedral : 29.582 168.627 4261 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1172 helix: 1.38 (0.19), residues: 720 sheet: 0.27 (0.73), residues: 53 loop : -0.54 (0.29), residues: 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.431 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 122 average time/residue: 1.7208 time to fit residues: 226.8143 Evaluate side-chains 123 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.323 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.4310 time to fit residues: 4.6041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 118 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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: 0.8169 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 16363 Z= 0.181 Angle : 0.574 9.655 23360 Z= 0.339 Chirality : 0.038 0.168 2645 Planarity : 0.004 0.042 1948 Dihedral : 29.546 171.009 4261 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 1.57 % 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: 1.48 (0.24), residues: 1172 helix: 1.78 (0.19), residues: 720 sheet: 0.36 (0.75), residues: 53 loop : -0.36 (0.29), residues: 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.287 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 121 average time/residue: 1.6614 time to fit residues: 217.9871 Evaluate side-chains 120 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 1.399 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.4228 time to fit residues: 4.4341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8229 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.061 16363 Z= 0.422 Angle : 0.635 9.063 23360 Z= 0.367 Chirality : 0.043 0.177 2645 Planarity : 0.005 0.049 1948 Dihedral : 29.581 170.487 4261 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 1.28 % 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: 1.07 (0.24), residues: 1172 helix: 1.44 (0.19), residues: 720 sheet: 0.26 (0.73), residues: 53 loop : -0.51 (0.29), residues: 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.412 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 120 average time/residue: 1.6432 time to fit residues: 213.7099 Evaluate side-chains 121 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.336 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.4677 time to fit residues: 3.4175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 140 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8180 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 16363 Z= 0.188 Angle : 0.579 10.392 23360 Z= 0.341 Chirality : 0.038 0.179 2645 Planarity : 0.004 0.045 1948 Dihedral : 29.552 172.494 4261 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 1.18 % 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: 1.37 (0.24), residues: 1172 helix: 1.68 (0.19), residues: 720 sheet: 0.31 (0.75), residues: 53 loop : -0.37 (0.29), residues: 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.277 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 116 average time/residue: 1.6847 time to fit residues: 211.4232 Evaluate side-chains 119 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 1.281 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.4043 time to fit residues: 3.7287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 112 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.198138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.156256 restraints weight = 30118.743| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.96 r_work: 0.3480 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work: 0.3315 rms_B_bonded: 4.62 restraints_weight: 0.1250 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4169 r_free = 0.4169 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4169 r_free = 0.4169 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 16363 Z= 0.227 Angle : 0.559 8.457 23360 Z= 0.328 Chirality : 0.037 0.168 2645 Planarity : 0.004 0.046 1948 Dihedral : 29.352 174.269 4261 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 1.18 % 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: 1.51 (0.24), residues: 1172 helix: 1.77 (0.19), residues: 720 sheet: 0.35 (0.75), residues: 53 loop : -0.28 (0.29), residues: 399 =============================================================================== Job complete usr+sys time: 3871.63 seconds wall clock time: 70 minutes 11.32 seconds (4211.32 seconds total)