Starting phenix.real_space_refine (version: dev) on Tue Apr 5 02:56:05 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g19_4338/04_2022/6g19_4338_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g19_4338/04_2022/6g19_4338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g19_4338/04_2022/6g19_4338.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g19_4338/04_2022/6g19_4338.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g19_4338/04_2022/6g19_4338_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g19_4338/04_2022/6g19_4338_updated.pdb" } resolution = 3.68 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= 0.014 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 Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 806": "NH1" <-> "NH2" Residue "A TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 942": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 10503 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 9874 Classifications: {'peptide': 682} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 661} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "X" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 308 Classifications: {'RNA': 14} Modifications used: {'rna3p_pyr': 3, 'rna3p_pur': 11} Link IDs: {'rna3p': 13} Chain: "Y" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 289 Classifications: {'RNA': 14} Modifications used: {'rna3p_pyr': 11, 'rna3p_pur': 3} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8332 SG CYS A 907 76.675 29.214 39.358 1.00 65.66 S ATOM 8379 SG CYS A 910 80.223 28.202 39.486 1.00 67.22 S ATOM 9041 SG CYS A 962 79.043 29.305 42.876 1.00 65.66 S ATOM 9060 SG CYS A 964 79.343 31.478 40.866 1.00 66.49 S Time building chain proxies: 6.02, per 1000 atoms: 0.57 Number of scatterers: 10503 At special positions: 0 Unit cell: (101.65, 87.74, 69.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 35 16.00 P 31 15.00 O 1227 8.00 N 1063 7.00 C 3744 6.00 H 4402 1.00 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: 10.34 Conformation dependent library (CDL) restraints added in 956.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 907 " Number of angles added : 6 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1304 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 6 sheets defined 43.5% alpha, 9.1% beta 14 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 4.86 Creating SS restraints... Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.809A pdb=" N GLU A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Proline residue: A 319 - end of helix Processing helix chain 'A' and resid 336 through 353 Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 379 through 382 No H-bonds generated for 'chain 'A' and resid 379 through 382' Processing helix chain 'A' and resid 401 through 404 No H-bonds generated for 'chain 'A' and resid 401 through 404' Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 457 through 473 Processing helix chain 'A' and resid 500 through 514 Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 551 through 566 removed outlier: 4.181A pdb=" N ILE A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 593 Processing helix chain 'A' and resid 599 through 615 removed outlier: 3.750A pdb=" N LYS A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 642 Processing helix chain 'A' and resid 671 through 681 Processing helix chain 'A' and resid 684 through 691 Processing helix chain 'A' and resid 694 through 696 No H-bonds generated for 'chain 'A' and resid 694 through 696' Processing helix chain 'A' and resid 700 through 714 removed outlier: 3.547A pdb=" N GLN A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 740 Processing helix chain 'A' and resid 742 through 746 Processing helix chain 'A' and resid 768 through 780 Processing helix chain 'A' and resid 813 through 820 Processing helix chain 'A' and resid 841 through 862 removed outlier: 3.812A pdb=" N TYR A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 882 Processing helix chain 'A' and resid 886 through 889 No H-bonds generated for 'chain 'A' and resid 886 through 889' Processing helix chain 'A' and resid 933 through 937 Processing sheet with id= A, first strand: chain 'A' and resid 326 through 329 removed outlier: 6.471A pdb=" N ILE A 441 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU A 488 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE A 443 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 537 through 542 removed outlier: 3.535A pdb=" N THR A 834 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 721 through 724 Processing sheet with id= D, first strand: chain 'A' and resid 987 through 991 removed outlier: 5.396A pdb=" N CYS A 907 " --> pdb=" O LEU A 913 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 913 " --> pdb=" O CYS A 907 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 920 through 923 Processing sheet with id= F, first strand: chain 'A' and resid 940 through 942 removed outlier: 3.723A pdb=" N GLU A 959 " --> pdb=" O ARG A 942 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 654 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 10.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 4391 1.01 - 1.21: 11 1.21 - 1.41: 2456 1.41 - 1.61: 3742 1.61 - 1.81: 58 Bond restraints: 10658 Sorted by residual: bond pdb=" O3A ANP A1102 " pdb=" PB ANP A1102 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" N3B ANP A1102 " pdb=" PG ANP A1102 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" CG ASN A 897 " pdb=" ND2 ASN A 897 " ideal model delta sigma weight residual 1.328 1.248 0.080 2.10e-02 2.27e+03 1.46e+01 bond pdb=" CB TYR A 455 " pdb=" CG TYR A 455 " ideal model delta sigma weight residual 1.512 1.434 0.078 2.20e-02 2.07e+03 1.24e+01 bond pdb=" O5' ANP A1102 " pdb=" PA ANP A1102 " ideal model delta sigma weight residual 1.655 1.585 0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 10653 not shown) Histogram of bond angle deviations from ideal: 60.05 - 76.68: 14 76.68 - 93.31: 0 93.31 - 109.93: 7660 109.93 - 126.56: 10803 126.56 - 143.19: 145 Bond angle restraints: 18622 Sorted by residual: angle pdb=" C MET A 886 " pdb=" N LYS A 887 " pdb=" H LYS A 887 " ideal model delta sigma weight residual 125.01 70.24 54.77 3.00e+00 1.11e-01 3.33e+02 angle pdb=" CA LYS A 887 " pdb=" N LYS A 887 " pdb=" H LYS A 887 " ideal model delta sigma weight residual 114.71 60.05 54.66 3.00e+00 1.11e-01 3.32e+02 angle pdb=" C LYS A 884 " pdb=" N LYS A 885 " pdb=" H LYS A 885 " ideal model delta sigma weight residual 124.88 70.39 54.49 3.00e+00 1.11e-01 3.30e+02 angle pdb=" C LYS A 887 " pdb=" N VAL A 888 " pdb=" H VAL A 888 " ideal model delta sigma weight residual 125.00 71.06 53.94 3.00e+00 1.11e-01 3.23e+02 angle pdb=" CA VAL A 888 " pdb=" N VAL A 888 " pdb=" H VAL A 888 " ideal model delta sigma weight residual 114.70 61.07 53.63 3.00e+00 1.11e-01 3.20e+02 ... (remaining 18617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.19: 4432 18.19 - 36.39: 153 36.39 - 54.58: 15 54.58 - 72.78: 6 72.78 - 90.97: 3 Dihedral angle restraints: 4609 sinusoidal: 2343 harmonic: 2266 Sorted by residual: dihedral pdb=" CA VAL A 454 " pdb=" C VAL A 454 " pdb=" N TYR A 455 " pdb=" CA TYR A 455 " ideal model delta harmonic sigma weight residual 180.00 93.60 86.40 0 5.00e+00 4.00e-02 2.99e+02 dihedral pdb=" CA GLU A 793 " pdb=" C GLU A 793 " pdb=" N GLU A 794 " pdb=" CA GLU A 794 " ideal model delta harmonic sigma weight residual 180.00 142.00 38.00 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CA GLU A 548 " pdb=" C GLU A 548 " pdb=" N ASN A 549 " pdb=" CA ASN A 549 " ideal model delta harmonic sigma weight residual -180.00 -145.43 -34.57 0 5.00e+00 4.00e-02 4.78e+01 ... (remaining 4606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 694 0.055 - 0.109: 229 0.109 - 0.164: 50 0.164 - 0.219: 12 0.219 - 0.273: 2 Chirality restraints: 987 Sorted by residual: chirality pdb=" CB VAL A 929 " pdb=" CA VAL A 929 " pdb=" CG1 VAL A 929 " pdb=" CG2 VAL A 929 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3' ANP A1102 " pdb=" C2' ANP A1102 " pdb=" C4' ANP A1102 " pdb=" O3' ANP A1102 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB VAL A 494 " pdb=" CA VAL A 494 " pdb=" CG1 VAL A 494 " pdb=" CG2 VAL A 494 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 984 not shown) Planarity restraints: 1564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 455 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C TYR A 455 " -0.060 2.00e-02 2.50e+03 pdb=" O TYR A 455 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN A 456 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 599 " 0.160 9.50e-02 1.11e+02 5.67e-02 1.10e+01 pdb=" NE ARG A 599 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 599 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 599 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 599 " 0.037 2.00e-02 2.50e+03 pdb="HH11 ARG A 599 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 599 " -0.022 2.00e-02 2.50e+03 pdb="HH21 ARG A 599 " -0.025 2.00e-02 2.50e+03 pdb="HH22 ARG A 599 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 944 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.22e+00 pdb=" CG ASN A 944 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 944 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 944 " -0.012 2.00e-02 2.50e+03 ... (remaining 1561 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 369 2.18 - 2.78: 18978 2.78 - 3.39: 24824 3.39 - 3.99: 33716 3.99 - 4.60: 53553 Nonbonded interactions: 131440 Sorted by model distance: nonbonded pdb=" H LYS A 498 " pdb=" HA LYS A 498 " model vdw 1.573 1.816 nonbonded pdb=" H VAL A 888 " pdb=" HA VAL A 888 " model vdw 1.578 1.816 nonbonded pdb=" H LYS A 887 " pdb=" HA LYS A 887 " model vdw 1.612 1.816 nonbonded pdb=" H LYS A 885 " pdb=" HA LYS A 885 " model vdw 1.650 1.816 nonbonded pdb=" H GLY A 795 " pdb=" HA3 GLY A 795 " model vdw 1.652 1.816 ... (remaining 131435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 31 5.49 5 S 35 5.16 5 C 3744 2.51 5 N 1063 2.21 5 O 1227 1.98 5 H 4402 0.53 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.170 Extract box with map and model: 3.450 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.100 Process input model: 45.740 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.013 0.144 6256 Z= 0.818 Angle : 1.149 20.876 8553 Z= 0.614 Chirality : 0.057 0.273 987 Planarity : 0.006 0.086 979 Dihedral : 10.381 90.973 2487 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.24 % Favored : 89.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.76 % 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: -4.18 (0.27), residues: 674 helix: -1.69 (0.24), residues: 332 sheet: -3.14 (0.46), residues: 89 loop : -4.04 (0.31), residues: 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3982 time to fit residues: 90.5816 Evaluate side-chains 93 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN A 457 ASN A 563 GLN A 678 ASN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6256 Z= 0.186 Angle : 0.743 21.411 8553 Z= 0.408 Chirality : 0.040 0.161 987 Planarity : 0.005 0.113 979 Dihedral : 8.124 81.271 1062 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.84 (0.30), residues: 674 helix: -0.20 (0.27), residues: 330 sheet: -2.70 (0.47), residues: 92 loop : -3.91 (0.33), residues: 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 104 average time/residue: 0.3253 time to fit residues: 45.2285 Evaluate side-chains 89 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.953 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2193 time to fit residues: 4.0849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN A 862 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 6256 Z= 0.151 Angle : 0.694 21.261 8553 Z= 0.382 Chirality : 0.038 0.159 987 Planarity : 0.003 0.038 979 Dihedral : 7.443 74.563 1062 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.61 % Favored : 91.25 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.72 (0.32), residues: 674 helix: 0.86 (0.28), residues: 333 sheet: -2.36 (0.48), residues: 97 loop : -3.57 (0.35), residues: 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 94 average time/residue: 0.3111 time to fit residues: 39.4881 Evaluate side-chains 79 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1381 time to fit residues: 1.8490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 0.0270 chunk 38 optimal weight: 0.7980 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 6256 Z= 0.141 Angle : 0.681 21.255 8553 Z= 0.377 Chirality : 0.037 0.154 987 Planarity : 0.003 0.036 979 Dihedral : 7.149 70.389 1062 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.25 (0.33), residues: 674 helix: 1.31 (0.29), residues: 333 sheet: -2.09 (0.50), residues: 97 loop : -3.47 (0.35), residues: 244 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.3187 time to fit residues: 34.3891 Evaluate side-chains 71 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 6256 Z= 0.262 Angle : 0.739 21.415 8553 Z= 0.407 Chirality : 0.040 0.147 987 Planarity : 0.003 0.030 979 Dihedral : 7.779 71.045 1062 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.50 % Favored : 90.36 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.16 (0.33), residues: 674 helix: 1.37 (0.29), residues: 333 sheet: -2.18 (0.50), residues: 101 loop : -3.34 (0.35), residues: 240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 84 average time/residue: 0.3086 time to fit residues: 35.6048 Evaluate side-chains 79 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1435 time to fit residues: 2.2292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.1980 chunk 67 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 6256 Z= 0.146 Angle : 0.677 21.171 8553 Z= 0.375 Chirality : 0.037 0.150 987 Planarity : 0.002 0.031 979 Dihedral : 7.118 69.739 1062 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.34), residues: 674 helix: 1.63 (0.29), residues: 334 sheet: -1.90 (0.52), residues: 99 loop : -3.29 (0.35), residues: 241 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 80 average time/residue: 0.2934 time to fit residues: 32.6326 Evaluate side-chains 76 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1289 time to fit residues: 1.8158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 6256 Z= 0.222 Angle : 0.704 21.192 8553 Z= 0.390 Chirality : 0.038 0.147 987 Planarity : 0.003 0.028 979 Dihedral : 7.429 71.959 1062 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.50 % Favored : 90.36 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.79 (0.34), residues: 674 helix: 1.68 (0.29), residues: 333 sheet: -1.53 (0.55), residues: 94 loop : -3.38 (0.34), residues: 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 85 average time/residue: 0.2919 time to fit residues: 34.6315 Evaluate side-chains 77 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1538 time to fit residues: 1.7159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 0.0770 chunk 45 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 6256 Z= 0.140 Angle : 0.676 21.110 8553 Z= 0.376 Chirality : 0.037 0.151 987 Planarity : 0.003 0.047 979 Dihedral : 6.920 69.450 1062 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.61 (0.34), residues: 674 helix: 1.79 (0.29), residues: 333 sheet: -1.32 (0.56), residues: 94 loop : -3.30 (0.35), residues: 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.3144 time to fit residues: 35.5964 Evaluate side-chains 73 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 6256 Z= 0.140 Angle : 0.662 21.058 8553 Z= 0.367 Chirality : 0.037 0.149 987 Planarity : 0.003 0.035 979 Dihedral : 6.737 69.394 1062 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.42 (0.34), residues: 674 helix: 1.96 (0.29), residues: 334 sheet: -1.23 (0.56), residues: 94 loop : -3.26 (0.35), residues: 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 82 average time/residue: 0.2953 time to fit residues: 33.6432 Evaluate side-chains 79 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.921 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2116 time to fit residues: 1.5007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 6256 Z= 0.170 Angle : 0.678 21.147 8553 Z= 0.377 Chirality : 0.037 0.146 987 Planarity : 0.003 0.033 979 Dihedral : 6.836 68.277 1062 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.44 (0.34), residues: 674 helix: 1.93 (0.29), residues: 334 sheet: -1.21 (0.56), residues: 94 loop : -3.25 (0.35), residues: 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1348 Ramachandran restraints generated. 674 Oldfield, 0 Emsley, 674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 381 is missing expected H atoms. Skipping. Residue LEU 397 is missing expected H atoms. Skipping. Residue LYS 398 is missing expected H atoms. Skipping. Residue ILE 399 is missing expected H atoms. Skipping. Residue LYS 406 is missing expected H atoms. Skipping. Residue LYS 451 is missing expected H atoms. Skipping. Residue LEU 463 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue LYS 474 is missing expected H atoms. Skipping. Residue LYS 498 is missing expected H atoms. Skipping. Residue LYS 505 is missing expected H atoms. Skipping. Residue LYS 538 is missing expected H atoms. Skipping. Residue LYS 552 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue MET 571 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 607 is missing expected H atoms. Skipping. Residue MET 620 is missing expected H atoms. Skipping. Residue LEU 669 is missing expected H atoms. Skipping. Residue LYS 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue MET 686 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 689 is missing expected H atoms. Skipping. Residue LYS 700 is missing expected H atoms. Skipping. Residue MET 739 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue LYS 764 is missing expected H atoms. Skipping. Residue ILE 783 is missing expected H atoms. Skipping. Residue LEU 785 is missing expected H atoms. Skipping. Residue LEU 786 is missing expected H atoms. Skipping. Residue ILE 787 is missing expected H atoms. Skipping. Residue ALA 788 is missing expected H atoms. Skipping. Residue THR 789 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 799 is missing expected H atoms. Skipping. Residue SER 828 is missing expected H atoms. Skipping. Residue THR 834 is missing expected H atoms. Skipping. Residue SER 835 is missing expected H atoms. Skipping. Residue SER 836 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 856 is missing expected H atoms. Skipping. Residue SER 880 is missing expected H atoms. Skipping. Residue ILE 881 is missing expected H atoms. Skipping. Residue LEU 882 is missing expected H atoms. Skipping. Residue LYS 884 is missing expected H atoms. Skipping. Residue LYS 885 is missing expected H atoms. Skipping. Residue MET 886 is missing expected H atoms. Skipping. Residue LYS 887 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue LYS 963 is missing expected H atoms. Skipping. Residue MET 972 is missing expected H atoms. Skipping. Residue VAL 973 is missing expected H atoms. Skipping. Residue LYS 975 is missing expected H atoms. Skipping. Residue LEU 979 is missing expected H atoms. Skipping. Residue LEU 1013 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.3052 time to fit residues: 34.3425 Evaluate side-chains 77 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 0.0470 chunk 23 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123660 restraints weight = 23076.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128338 restraints weight = 10658.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131249 restraints weight = 6414.765| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 6256 Z= 0.132 Angle : 0.663 21.063 8553 Z= 0.367 Chirality : 0.037 0.152 987 Planarity : 0.002 0.030 979 Dihedral : 6.524 68.442 1062 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.29 (0.35), residues: 674 helix: 2.05 (0.29), residues: 334 sheet: -1.44 (0.54), residues: 100 loop : -3.05 (0.36), residues: 240 =============================================================================== Job complete usr+sys time: 2481.97 seconds wall clock time: 44 minutes 57.37 seconds (2697.37 seconds total)