Starting phenix.real_space_refine on Wed Feb 14 23:02:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g19_4338/02_2024/6g19_4338_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g19_4338/02_2024/6g19_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_4338/02_2024/6g19_4338.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g19_4338/02_2024/6g19_4338.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g19_4338/02_2024/6g19_4338_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g19_4338/02_2024/6g19_4338_updated.pdb" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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 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. 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-5238/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_pur': 11, 'rna3p_pyr': 3} 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_pur': 3, 'rna3p_pyr': 11} 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: 5.63, per 1000 atoms: 0.54 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: 8.51 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal 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: 5.66 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: 3.89 Time building geometry restraints manager: 8.79 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: 5061 18.19 - 36.39: 217 36.39 - 54.58: 53 54.58 - 72.78: 43 72.78 - 90.97: 15 Dihedral angle restraints: 5389 sinusoidal: 3123 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 5386 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 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: 0.800 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: 0.180 Extract box with map and model: 2.930 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 44.270 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 : 14.452 90.973 2625 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 % Allowed : 3.45 % Favored : 96.55 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 737 HIS 0.011 0.002 HIS A 506 PHE 0.014 0.002 PHE A 517 TYR 0.025 0.003 TYR A 455 ARG 0.014 0.001 ARG A 619 *********************** 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 : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.7951 (m) cc_final: 0.7657 (p) REVERT: A 515 ASP cc_start: 0.7569 (t0) cc_final: 0.7350 (t0) REVERT: A 639 PHE cc_start: 0.7356 (m-10) cc_final: 0.6745 (t80) REVERT: A 959 GLU cc_start: 0.7590 (tt0) cc_final: 0.7195 (mt-10) REVERT: A 973 VAL cc_start: 0.9014 (t) cc_final: 0.8664 (m) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.4111 time to fit residues: 91.9925 Evaluate side-chains 95 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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: 0.9980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7685 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6256 Z= 0.177 Angle : 0.743 21.436 8553 Z= 0.406 Chirality : 0.039 0.160 987 Planarity : 0.005 0.112 979 Dihedral : 16.022 84.411 1200 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.20 % Favored : 90.65 % Rotamer: Outliers : 2.30 % Allowed : 9.05 % Favored : 88.65 % 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: -2.71 (0.30), residues: 674 helix: -0.08 (0.27), residues: 330 sheet: -2.64 (0.48), residues: 92 loop : -3.87 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 968 HIS 0.004 0.001 HIS A 626 PHE 0.015 0.001 PHE A 551 TYR 0.017 0.002 TYR A 342 ARG 0.010 0.001 ARG A 599 *********************** 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 113 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.954 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: A 400 SER cc_start: 0.7941 (m) cc_final: 0.7460 (p) REVERT: A 639 PHE cc_start: 0.7262 (m-10) cc_final: 0.6772 (t80) REVERT: A 854 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7540 (ptt) REVERT: A 973 VAL cc_start: 0.8989 (t) cc_final: 0.8649 (m) outliers start: 14 outliers final: 8 residues processed: 105 average time/residue: 0.3334 time to fit residues: 46.6910 Evaluate side-chains 92 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 854 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7769 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6256 Z= 0.213 Angle : 0.714 21.354 8553 Z= 0.394 Chirality : 0.039 0.149 987 Planarity : 0.004 0.040 979 Dihedral : 15.448 87.500 1200 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.61 % Favored : 91.25 % Rotamer: Outliers : 1.48 % Allowed : 11.68 % Favored : 86.84 % 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: -1.86 (0.32), residues: 674 helix: 0.74 (0.28), residues: 333 sheet: -2.47 (0.47), residues: 99 loop : -3.59 (0.34), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 968 HIS 0.007 0.001 HIS A 506 PHE 0.010 0.001 PHE A 551 TYR 0.014 0.001 TYR A 455 ARG 0.003 0.000 ARG A 843 *********************** 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 107 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.978 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: A 400 SER cc_start: 0.8025 (m) cc_final: 0.7556 (p) REVERT: A 437 ASP cc_start: 0.5666 (m-30) cc_final: 0.5129 (m-30) REVERT: A 639 PHE cc_start: 0.7355 (m-10) cc_final: 0.6859 (t80) REVERT: A 864 MET cc_start: 0.7501 (ttm) cc_final: 0.7290 (ttm) REVERT: A 973 VAL cc_start: 0.9175 (t) cc_final: 0.8934 (m) outliers start: 9 outliers final: 5 residues processed: 100 average time/residue: 0.3313 time to fit residues: 44.7624 Evaluate side-chains 89 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 979 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 7 optimal weight: 0.0980 chunk 30 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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: 0.7818 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6256 Z= 0.225 Angle : 0.717 21.320 8553 Z= 0.396 Chirality : 0.039 0.149 987 Planarity : 0.003 0.038 979 Dihedral : 15.312 87.317 1200 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.35 % Favored : 90.50 % Rotamer: Outliers : 1.97 % Allowed : 12.34 % Favored : 85.69 % 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: -1.42 (0.33), residues: 674 helix: 1.14 (0.29), residues: 333 sheet: -2.23 (0.49), residues: 99 loop : -3.48 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 968 HIS 0.006 0.001 HIS A 506 PHE 0.013 0.001 PHE A 401 TYR 0.014 0.001 TYR A 455 ARG 0.003 0.000 ARG A 843 *********************** 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 97 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.937 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: A 639 PHE cc_start: 0.7452 (m-10) cc_final: 0.6997 (t80) outliers start: 12 outliers final: 10 residues processed: 91 average time/residue: 0.3048 time to fit residues: 38.0350 Evaluate side-chains 87 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 836 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 60 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 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 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6256 Z= 0.166 Angle : 0.684 21.107 8553 Z= 0.378 Chirality : 0.038 0.150 987 Planarity : 0.003 0.036 979 Dihedral : 15.276 86.533 1200 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.16 % Favored : 91.69 % Rotamer: Outliers : 1.64 % Allowed : 13.65 % Favored : 84.70 % 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: -1.08 (0.33), residues: 674 helix: 1.41 (0.29), residues: 334 sheet: -1.95 (0.51), residues: 97 loop : -3.37 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 582 HIS 0.004 0.001 HIS A 506 PHE 0.009 0.001 PHE A 401 TYR 0.011 0.001 TYR A 455 ARG 0.002 0.000 ARG A 843 *********************** 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 95 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.7959 (m) cc_final: 0.7539 (p) REVERT: A 639 PHE cc_start: 0.7509 (m-10) cc_final: 0.7049 (t80) REVERT: A 722 ILE cc_start: 0.8439 (mp) cc_final: 0.8199 (mt) REVERT: A 762 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6919 (pt0) REVERT: A 973 VAL cc_start: 0.9179 (t) cc_final: 0.8845 (m) outliers start: 10 outliers final: 8 residues processed: 92 average time/residue: 0.3212 time to fit residues: 41.1707 Evaluate side-chains 86 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 979 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 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 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: 0.7818 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6256 Z= 0.175 Angle : 0.683 21.141 8553 Z= 0.377 Chirality : 0.037 0.146 987 Planarity : 0.003 0.034 979 Dihedral : 15.258 85.094 1200 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.14 % Allowed : 13.98 % Favored : 83.88 % 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: -0.82 (0.34), residues: 674 helix: 1.62 (0.29), residues: 334 sheet: -1.49 (0.54), residues: 92 loop : -3.38 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 582 HIS 0.005 0.001 HIS A 506 PHE 0.013 0.001 PHE A 401 TYR 0.015 0.001 TYR A 342 ARG 0.004 0.000 ARG A 714 *********************** 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 95 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.7973 (m) cc_final: 0.7574 (p) REVERT: A 610 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.5607 (mp0) REVERT: A 639 PHE cc_start: 0.7518 (m-10) cc_final: 0.7063 (t80) REVERT: A 762 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6966 (pt0) REVERT: A 973 VAL cc_start: 0.9377 (t) cc_final: 0.9025 (m) outliers start: 13 outliers final: 10 residues processed: 89 average time/residue: 0.3270 time to fit residues: 39.8238 Evaluate side-chains 87 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 979 LEU 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: 4.9990 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** ** 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: 0.7833 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6256 Z= 0.183 Angle : 0.681 21.169 8553 Z= 0.376 Chirality : 0.037 0.146 987 Planarity : 0.003 0.037 979 Dihedral : 15.187 84.817 1200 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 1.81 % Allowed : 15.62 % Favored : 82.57 % 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: -0.70 (0.34), residues: 674 helix: 1.72 (0.29), residues: 333 sheet: -1.45 (0.54), residues: 94 loop : -3.30 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 385 HIS 0.004 0.001 HIS A 506 PHE 0.010 0.001 PHE A 401 TYR 0.014 0.001 TYR A 342 ARG 0.007 0.001 ARG A 375 *********************** 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 97 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.7994 (m) cc_final: 0.7619 (p) REVERT: A 586 MET cc_start: 0.8222 (ttp) cc_final: 0.8007 (tmm) REVERT: A 639 PHE cc_start: 0.7516 (m-10) cc_final: 0.7073 (t80) REVERT: A 762 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6973 (pt0) REVERT: A 973 VAL cc_start: 0.9289 (t) cc_final: 0.9087 (m) outliers start: 11 outliers final: 9 residues processed: 91 average time/residue: 0.3148 time to fit residues: 38.9182 Evaluate side-chains 87 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 979 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 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: 0.7849 moved from start: 0.5135 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= 0.200 Angle : 0.688 21.187 8553 Z= 0.380 Chirality : 0.038 0.147 987 Planarity : 0.003 0.036 979 Dihedral : 15.176 84.858 1200 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 1.64 % Allowed : 16.12 % Favored : 82.24 % 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: -0.71 (0.34), residues: 674 helix: 1.70 (0.29), residues: 334 sheet: -1.46 (0.53), residues: 94 loop : -3.30 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 385 HIS 0.004 0.001 HIS A 506 PHE 0.011 0.001 PHE A 401 TYR 0.012 0.001 TYR A 342 ARG 0.005 0.000 ARG A 375 *********************** 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 94 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.8003 (m) cc_final: 0.7630 (p) REVERT: A 639 PHE cc_start: 0.7476 (m-10) cc_final: 0.7069 (t80) REVERT: A 762 GLU cc_start: 0.7264 (mt-10) cc_final: 0.7014 (pt0) outliers start: 10 outliers final: 10 residues processed: 89 average time/residue: 0.3245 time to fit residues: 39.9140 Evaluate side-chains 89 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 979 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 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: 0.7844 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6256 Z= 0.182 Angle : 0.684 21.121 8553 Z= 0.379 Chirality : 0.037 0.145 987 Planarity : 0.003 0.039 979 Dihedral : 15.159 84.931 1200 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 1.48 % Allowed : 16.61 % Favored : 81.91 % 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: 1.76 (0.29), residues: 334 sheet: -1.39 (0.54), residues: 94 loop : -3.23 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 968 HIS 0.003 0.001 HIS A 506 PHE 0.009 0.001 PHE A 401 TYR 0.013 0.001 TYR A 342 ARG 0.007 0.000 ARG A 375 *********************** 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 94 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.7986 (m) cc_final: 0.7615 (p) REVERT: A 639 PHE cc_start: 0.7477 (m-10) cc_final: 0.7082 (t80) REVERT: A 762 GLU cc_start: 0.7221 (mt-10) cc_final: 0.7014 (pt0) REVERT: A 764 LYS cc_start: 0.8638 (ttpp) cc_final: 0.7765 (mptt) outliers start: 9 outliers final: 9 residues processed: 91 average time/residue: 0.3604 time to fit residues: 44.5240 Evaluate side-chains 89 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 979 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 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: 0.7838 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6256 Z= 0.171 Angle : 0.676 21.155 8553 Z= 0.374 Chirality : 0.037 0.147 987 Planarity : 0.003 0.044 979 Dihedral : 15.140 85.082 1200 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 1.48 % Allowed : 16.78 % Favored : 81.74 % 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: -0.52 (0.34), residues: 674 helix: 1.86 (0.29), residues: 335 sheet: -1.38 (0.55), residues: 95 loop : -3.23 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 968 HIS 0.003 0.001 HIS A 506 PHE 0.009 0.001 PHE A 401 TYR 0.013 0.001 TYR A 342 ARG 0.006 0.000 ARG A 375 ********************** 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 90 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.7990 (m) cc_final: 0.7628 (p) REVERT: A 639 PHE cc_start: 0.7380 (m-10) cc_final: 0.7011 (t80) REVERT: A 762 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6993 (pt0) REVERT: A 764 LYS cc_start: 0.8689 (ttpp) cc_final: 0.7862 (mptt) outliers start: 9 outliers final: 9 residues processed: 86 average time/residue: 0.3369 time to fit residues: 38.9360 Evaluate side-chains 85 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 979 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 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 = 0.3583 r_free = 0.3583 target = 0.134472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115595 restraints weight = 23462.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119949 restraints weight = 11079.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122683 restraints weight = 6861.304| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6256 Z= 0.285 Angle : 0.734 21.088 8553 Z= 0.404 Chirality : 0.039 0.144 987 Planarity : 0.003 0.036 979 Dihedral : 15.258 86.974 1200 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 1.64 % Allowed : 17.27 % Favored : 81.09 % 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: -0.82 (0.33), residues: 674 helix: 1.58 (0.29), residues: 335 sheet: -1.49 (0.55), residues: 95 loop : -3.35 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 385 HIS 0.004 0.001 HIS A 506 PHE 0.012 0.001 PHE A 401 TYR 0.012 0.001 TYR A 342 ARG 0.007 0.001 ARG A 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2638.73 seconds wall clock time: 47 minutes 55.15 seconds (2875.15 seconds total)