Starting phenix.real_space_refine on Tue Feb 13 09:38:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c07_16356/02_2024/8c07_16356_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c07_16356/02_2024/8c07_16356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c07_16356/02_2024/8c07_16356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c07_16356/02_2024/8c07_16356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c07_16356/02_2024/8c07_16356_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c07_16356/02_2024/8c07_16356_updated.pdb" } resolution = 3.3 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 3159 2.51 5 N 875 2.21 5 O 921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 2027": "OD1" <-> "OD2" Residue "B GLU 2222": "OE1" <-> "OE2" Residue "B GLU 2230": "OE1" <-> "OE2" Residue "B GLU 2287": "OE1" <-> "OE2" Residue "B GLU 2307": "OE1" <-> "OE2" Residue "B TYR 2576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2673": "OE1" <-> "OE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "J GLU 208": "OE1" <-> "OE2" 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: 4974 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3475 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 31, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "I" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "K" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 563 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 358 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'SY8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.34, per 1000 atoms: 0.67 Number of scatterers: 4974 At special positions: 0 Unit cell: (68.9472, 90.2272, 102.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 921 8.00 N 875 7.00 C 3159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of additional links: simple=1, symmetry=0 Simple link: pdb=" C GLY K 75 " - pdb=" N SY8 K 101 " Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 1.0 seconds 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1216 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 5 sheets defined 37.6% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'B' and resid 2027 through 2029 No H-bonds generated for 'chain 'B' and resid 2027 through 2029' Processing helix chain 'B' and resid 2044 through 2047 No H-bonds generated for 'chain 'B' and resid 2044 through 2047' Processing helix chain 'B' and resid 2049 through 2052 No H-bonds generated for 'chain 'B' and resid 2049 through 2052' Processing helix chain 'B' and resid 2064 through 2067 No H-bonds generated for 'chain 'B' and resid 2064 through 2067' Processing helix chain 'B' and resid 2218 through 2235 removed outlier: 3.630A pdb=" N LYS B2224 " --> pdb=" O VAL B2220 " (cutoff:3.500A) Processing helix chain 'B' and resid 2249 through 2258 Processing helix chain 'B' and resid 2290 through 2302 Processing helix chain 'B' and resid 2525 through 2530 Processing helix chain 'B' and resid 2533 through 2541 Processing helix chain 'B' and resid 2552 through 2559 Processing helix chain 'B' and resid 2565 through 2570 removed outlier: 3.615A pdb=" N ALA B2569 " --> pdb=" O HIS B2566 " (cutoff:3.500A) Processing helix chain 'B' and resid 2573 through 2587 removed outlier: 3.583A pdb=" N GLN B2587 " --> pdb=" O ILE B2583 " (cutoff:3.500A) Processing helix chain 'B' and resid 2595 through 2598 No H-bonds generated for 'chain 'B' and resid 2595 through 2598' Processing helix chain 'B' and resid 2628 through 2644 removed outlier: 3.688A pdb=" N VAL B2631 " --> pdb=" O PRO B2628 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR B2632 " --> pdb=" O GLN B2629 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B2637 " --> pdb=" O TYR B2634 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B2639 " --> pdb=" O ARG B2636 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B2640 " --> pdb=" O LYS B2637 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET B2643 " --> pdb=" O GLU B2640 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU B2644 " --> pdb=" O HIS B2641 " (cutoff:3.500A) Processing helix chain 'B' and resid 2648 through 2659 Processing helix chain 'B' and resid 2672 through 2677 Processing helix chain 'B' and resid 2687 through 2692 Processing helix chain 'B' and resid 2710 through 2719 Processing helix chain 'B' and resid 2723 through 2734 Processing helix chain 'B' and resid 2743 through 2745 No H-bonds generated for 'chain 'B' and resid 2743 through 2745' Processing helix chain 'B' and resid 2781 through 2792 removed outlier: 4.498A pdb=" N LYS B2792 " --> pdb=" O LEU B2788 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 32 Processing helix chain 'I' and resid 38 through 40 No H-bonds generated for 'chain 'I' and resid 38 through 40' Processing helix chain 'K' and resid 23 through 33 Processing helix chain 'K' and resid 38 through 40 No H-bonds generated for 'chain 'K' and resid 38 through 40' Processing helix chain 'K' and resid 56 through 59 removed outlier: 3.870A pdb=" N TYR K 59 " --> pdb=" O LEU K 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 56 through 59' Processing helix chain 'J' and resid 187 through 196 Processing helix chain 'J' and resid 202 through 211 Processing helix chain 'J' and resid 216 through 224 Processing sheet with id= A, first strand: chain 'B' and resid 2751 through 2754 Processing sheet with id= B, first strand: chain 'B' and resid 2238 through 2243 removed outlier: 7.353A pdb=" N LEU B2240 " --> pdb=" O HIS B2275 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL B2277 " --> pdb=" O LEU B2240 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU B2242 " --> pdb=" O VAL B2277 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL B2279 " --> pdb=" O LEU B2242 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'I' and resid 12 through 16 removed outlier: 4.229A pdb=" N ILE I 13 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL I 5 " --> pdb=" O ILE I 13 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU I 15 " --> pdb=" O ILE I 3 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE I 3 " --> pdb=" O LEU I 15 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I 69 " --> pdb=" O LYS I 6 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE I 44 " --> pdb=" O HIS I 68 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 3 through 6 removed outlier: 7.032A pdb=" N SER K 65 " --> pdb=" O PHE K 4 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LYS K 6 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU K 67 " --> pdb=" O LYS K 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'K' and resid 41 through 43 136 hydrogen bonds defined for protein. 375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1564 1.34 - 1.46: 679 1.46 - 1.57: 2795 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 5068 Sorted by residual: bond pdb=" N ASP B2027 " pdb=" CA ASP B2027 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.28e-02 6.10e+03 5.04e+00 bond pdb=" C ILE B2769 " pdb=" N SER B2770 " ideal model delta sigma weight residual 1.332 1.360 -0.027 1.40e-02 5.10e+03 3.83e+00 bond pdb=" N PHE B2796 " pdb=" CA PHE B2796 " ideal model delta sigma weight residual 1.467 1.487 -0.020 1.32e-02 5.74e+03 2.24e+00 bond pdb=" CA ILE B2769 " pdb=" CB ILE B2769 " ideal model delta sigma weight residual 1.540 1.559 -0.019 1.36e-02 5.41e+03 2.00e+00 bond pdb=" C GLN B2649 " pdb=" N PRO B2650 " ideal model delta sigma weight residual 1.335 1.353 -0.017 1.36e-02 5.41e+03 1.62e+00 ... (remaining 5063 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.74: 136 105.74 - 112.89: 2632 112.89 - 120.04: 1884 120.04 - 127.19: 2178 127.19 - 134.33: 42 Bond angle restraints: 6872 Sorted by residual: angle pdb=" CB ARG B2227 " pdb=" CG ARG B2227 " pdb=" CD ARG B2227 " ideal model delta sigma weight residual 111.30 122.69 -11.39 2.30e+00 1.89e-01 2.45e+01 angle pdb=" C ASP B2590 " pdb=" N ALA B2591 " pdb=" CA ALA B2591 " ideal model delta sigma weight residual 121.54 129.38 -7.84 1.91e+00 2.74e-01 1.68e+01 angle pdb=" CA ARG J 202 " pdb=" CB ARG J 202 " pdb=" CG ARG J 202 " ideal model delta sigma weight residual 114.10 121.76 -7.66 2.00e+00 2.50e-01 1.47e+01 angle pdb=" N PRO B2750 " pdb=" CA PRO B2750 " pdb=" C PRO B2750 " ideal model delta sigma weight residual 111.33 116.52 -5.19 1.43e+00 4.89e-01 1.32e+01 angle pdb=" N SER B2770 " pdb=" CA SER B2770 " pdb=" C SER B2770 " ideal model delta sigma weight residual 110.80 117.74 -6.94 2.13e+00 2.20e-01 1.06e+01 ... (remaining 6867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.40: 2935 28.40 - 56.80: 142 56.80 - 85.20: 12 85.20 - 113.60: 4 113.60 - 142.00: 3 Dihedral angle restraints: 3096 sinusoidal: 1231 harmonic: 1865 Sorted by residual: dihedral pdb=" CA MET B2643 " pdb=" C MET B2643 " pdb=" N LEU B2644 " pdb=" CA LEU B2644 " ideal model delta harmonic sigma weight residual 180.00 -155.26 -24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA SER B2770 " pdb=" C SER B2770 " pdb=" N ARG B2771 " pdb=" CA ARG B2771 " ideal model delta harmonic sigma weight residual -180.00 -156.89 -23.11 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" C1 SY8 K 101 " pdb=" C2 SY8 K 101 " pdb=" C3 SY8 K 101 " pdb=" C4 SY8 K 101 " ideal model delta sinusoidal sigma weight residual 57.79 -84.21 142.00 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 527 0.047 - 0.094: 188 0.094 - 0.140: 61 0.140 - 0.187: 9 0.187 - 0.234: 3 Chirality restraints: 788 Sorted by residual: chirality pdb=" CA ARG B2227 " pdb=" N ARG B2227 " pdb=" C ARG B2227 " pdb=" CB ARG B2227 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB ILE B2624 " pdb=" CA ILE B2624 " pdb=" CG1 ILE B2624 " pdb=" CG2 ILE B2624 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CG LEU B2606 " pdb=" CB LEU B2606 " pdb=" CD1 LEU B2606 " pdb=" CD2 LEU B2606 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.77e-01 ... (remaining 785 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B2774 " 0.073 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO B2775 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO B2775 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO B2775 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B2507 " -0.059 5.00e-02 4.00e+02 9.00e-02 1.30e+01 pdb=" N PRO B2508 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO B2508 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B2508 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B2627 " 0.049 5.00e-02 4.00e+02 7.43e-02 8.82e+00 pdb=" N PRO B2628 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO B2628 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B2628 " 0.041 5.00e-02 4.00e+02 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1355 2.81 - 3.33: 4267 3.33 - 3.86: 7754 3.86 - 4.38: 8535 4.38 - 4.90: 14644 Nonbonded interactions: 36555 Sorted by model distance: nonbonded pdb=" O ASN B2795 " pdb=" OD1 ASN B2795 " model vdw 2.288 3.040 nonbonded pdb=" O HIS B2761 " pdb=" OH TYR B2777 " model vdw 2.362 2.440 nonbonded pdb=" OG1 THR K 22 " pdb=" OD1 ASN K 25 " model vdw 2.362 2.440 nonbonded pdb=" O GLY B2683 " pdb=" OG SER B2738 " model vdw 2.383 2.440 nonbonded pdb=" O TYR B2731 " pdb=" NH2 ARG K 74 " model vdw 2.402 2.520 ... (remaining 36550 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'I' and (resid 1 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 10 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 28 or (resid 29 and (name \ N or name CA or name C or name O or name CB )) or resid 30 through 32 or (resid \ 33 and (name N or name CA or name C or name O or name CB )) or resid 34 through \ 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or res \ id 45 through 47 or resid 49 through 50 or (resid 51 through 52 and (name N or n \ ame CA or name C or name O or name CB )) or resid 53 or (resid 54 and (name N or \ name CA or name C or name O or name CB )) or resid 55 or (resid 56 and (name N \ or name CA or name C or name O or name CB )) or resid 57 through 72)) selection = (chain 'K' and (resid 1 through 47 or resid 49 through 72)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 26.380 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.370 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5068 Z= 0.267 Angle : 0.939 11.394 6872 Z= 0.491 Chirality : 0.054 0.234 788 Planarity : 0.010 0.111 902 Dihedral : 16.627 142.004 1879 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.38 % Allowed : 0.94 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.28), residues: 630 helix: -2.09 (0.26), residues: 256 sheet: -1.31 (0.85), residues: 43 loop : -1.97 (0.30), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B2733 HIS 0.003 0.001 HIS B2020 PHE 0.038 0.002 PHE B2218 TYR 0.013 0.002 TYR B2576 ARG 0.014 0.001 ARG B2227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.586 Fit side-chains REVERT: B 2666 SER cc_start: 0.7991 (p) cc_final: 0.7734 (p) REVERT: B 2743 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6945 (mm-30) outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 0.1865 time to fit residues: 24.5955 Evaluate side-chains 93 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2795 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.0020 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.0050 overall best weight: 0.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5068 Z= 0.160 Angle : 0.581 7.449 6872 Z= 0.299 Chirality : 0.042 0.150 788 Planarity : 0.007 0.072 902 Dihedral : 10.743 144.500 692 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 1.89 % Allowed : 12.45 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.32), residues: 630 helix: -1.11 (0.30), residues: 258 sheet: -1.43 (0.89), residues: 43 loop : -1.68 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B2565 HIS 0.002 0.001 HIS B2553 PHE 0.013 0.001 PHE B2710 TYR 0.008 0.001 TYR B2634 ARG 0.005 0.000 ARG B2227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.552 Fit side-chains REVERT: B 2643 MET cc_start: 0.7604 (mtt) cc_final: 0.7290 (mtt) REVERT: B 2666 SER cc_start: 0.8033 (p) cc_final: 0.7761 (p) REVERT: I 1 MET cc_start: 0.4139 (mmt) cc_final: 0.3893 (mmt) outliers start: 10 outliers final: 8 residues processed: 102 average time/residue: 0.1859 time to fit residues: 24.2066 Evaluate side-chains 105 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2261 ASN Chi-restraints excluded: chain B residue 2564 ASN Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain B residue 2795 ASN Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 15 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 56 optimal weight: 0.2980 chunk 19 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 overall best weight: 0.1576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5068 Z= 0.141 Angle : 0.538 6.932 6872 Z= 0.276 Chirality : 0.041 0.156 788 Planarity : 0.006 0.054 902 Dihedral : 10.349 162.448 692 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.26 % Allowed : 15.47 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.32), residues: 630 helix: -0.57 (0.32), residues: 255 sheet: -1.90 (0.95), residues: 35 loop : -1.65 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2565 HIS 0.002 0.000 HIS B2020 PHE 0.013 0.001 PHE B2218 TYR 0.008 0.001 TYR B2773 ARG 0.005 0.000 ARG B2227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.596 Fit side-chains REVERT: B 2575 MET cc_start: 0.5869 (tpp) cc_final: 0.5558 (tpp) REVERT: B 2666 SER cc_start: 0.8045 (p) cc_final: 0.7798 (p) outliers start: 12 outliers final: 9 residues processed: 100 average time/residue: 0.1954 time to fit residues: 24.5102 Evaluate side-chains 102 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2261 ASN Chi-restraints excluded: chain B residue 2301 GLN Chi-restraints excluded: chain B residue 2564 ASN Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.0050 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 54 optimal weight: 0.1980 chunk 16 optimal weight: 0.4980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2253 GLN B2795 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5068 Z= 0.189 Angle : 0.568 7.941 6872 Z= 0.290 Chirality : 0.042 0.161 788 Planarity : 0.005 0.049 902 Dihedral : 9.060 160.962 690 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.45 % Allowed : 18.11 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.32), residues: 630 helix: -0.23 (0.32), residues: 252 sheet: -1.47 (0.89), residues: 45 loop : -1.58 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B2565 HIS 0.002 0.001 HIS B2020 PHE 0.016 0.002 PHE B2218 TYR 0.007 0.001 TYR B2773 ARG 0.005 0.000 ARG B2227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: B 2575 MET cc_start: 0.6079 (tpp) cc_final: 0.5812 (tpp) REVERT: B 2666 SER cc_start: 0.8109 (p) cc_final: 0.7848 (p) outliers start: 13 outliers final: 12 residues processed: 99 average time/residue: 0.1799 time to fit residues: 22.5779 Evaluate side-chains 106 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2261 ASN Chi-restraints excluded: chain B residue 2301 GLN Chi-restraints excluded: chain B residue 2564 ASN Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2716 SER Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain K residue 27 LYS Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 42 optimal weight: 0.0170 chunk 31 optimal weight: 0.0970 chunk 54 optimal weight: 0.0870 chunk 15 optimal weight: 0.0050 chunk 20 optimal weight: 0.9980 overall best weight: 0.1408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5068 Z= 0.130 Angle : 0.522 7.434 6872 Z= 0.264 Chirality : 0.041 0.167 788 Planarity : 0.005 0.049 902 Dihedral : 6.704 129.604 690 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.08 % Allowed : 18.87 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.33), residues: 630 helix: 0.03 (0.33), residues: 250 sheet: -1.69 (0.86), residues: 47 loop : -1.42 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B2565 HIS 0.002 0.001 HIS B2020 PHE 0.013 0.001 PHE B2218 TYR 0.016 0.001 TYR B2576 ARG 0.003 0.000 ARG B2676 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: B 2666 SER cc_start: 0.8053 (p) cc_final: 0.7822 (p) outliers start: 11 outliers final: 9 residues processed: 101 average time/residue: 0.1984 time to fit residues: 25.1179 Evaluate side-chains 103 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2261 ASN Chi-restraints excluded: chain B residue 2301 GLN Chi-restraints excluded: chain B residue 2564 ASN Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain K residue 27 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.0870 chunk 12 optimal weight: 0.0040 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 0.0570 chunk 60 optimal weight: 0.0980 chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.0888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5068 Z= 0.127 Angle : 0.526 6.988 6872 Z= 0.265 Chirality : 0.040 0.174 788 Planarity : 0.005 0.048 902 Dihedral : 6.021 114.796 690 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.64 % Allowed : 19.25 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.33), residues: 630 helix: 0.18 (0.34), residues: 249 sheet: -2.12 (0.91), residues: 37 loop : -1.33 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B2565 HIS 0.002 0.000 HIS B2553 PHE 0.012 0.001 PHE B2693 TYR 0.013 0.001 TYR B2576 ARG 0.004 0.000 ARG B2676 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: B 2666 SER cc_start: 0.8036 (p) cc_final: 0.7806 (p) outliers start: 14 outliers final: 10 residues processed: 100 average time/residue: 0.1778 time to fit residues: 22.5140 Evaluate side-chains 103 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2261 ASN Chi-restraints excluded: chain B residue 2301 GLN Chi-restraints excluded: chain B residue 2304 LEU Chi-restraints excluded: chain B residue 2564 ASN Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain K residue 27 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 60 optimal weight: 0.1980 chunk 38 optimal weight: 0.1980 chunk 37 optimal weight: 0.0980 chunk 28 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 36 optimal weight: 0.0470 chunk 18 optimal weight: 0.0980 overall best weight: 0.1056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5068 Z= 0.125 Angle : 0.529 8.552 6872 Z= 0.264 Chirality : 0.041 0.177 788 Planarity : 0.005 0.048 902 Dihedral : 5.741 106.012 690 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.26 % Allowed : 19.25 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.34), residues: 630 helix: 0.32 (0.34), residues: 249 sheet: -2.07 (0.90), residues: 37 loop : -1.28 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B2565 HIS 0.002 0.001 HIS B2553 PHE 0.017 0.001 PHE B2218 TYR 0.014 0.001 TYR B2576 ARG 0.004 0.000 ARG B2676 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: B 2666 SER cc_start: 0.8043 (p) cc_final: 0.7818 (p) outliers start: 12 outliers final: 11 residues processed: 102 average time/residue: 0.1978 time to fit residues: 25.5456 Evaluate side-chains 107 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2052 ASP Chi-restraints excluded: chain B residue 2261 ASN Chi-restraints excluded: chain B residue 2304 LEU Chi-restraints excluded: chain B residue 2521 ASN Chi-restraints excluded: chain B residue 2564 ASN Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain K residue 27 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 chunk 55 optimal weight: 0.0570 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5068 Z= 0.194 Angle : 0.585 9.656 6872 Z= 0.295 Chirality : 0.042 0.182 788 Planarity : 0.005 0.049 902 Dihedral : 5.603 94.285 690 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.83 % Allowed : 19.81 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.33), residues: 630 helix: 0.20 (0.33), residues: 250 sheet: -1.92 (0.92), residues: 35 loop : -1.35 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B2565 HIS 0.002 0.001 HIS B2566 PHE 0.017 0.002 PHE B2218 TYR 0.014 0.001 TYR B2576 ARG 0.004 0.000 ARG B2227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: B 2666 SER cc_start: 0.8109 (p) cc_final: 0.7871 (p) REVERT: B 2684 GLU cc_start: 0.7457 (pm20) cc_final: 0.7236 (pm20) outliers start: 15 outliers final: 14 residues processed: 102 average time/residue: 0.1916 time to fit residues: 24.8403 Evaluate side-chains 111 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2052 ASP Chi-restraints excluded: chain B residue 2248 ARG Chi-restraints excluded: chain B residue 2261 ASN Chi-restraints excluded: chain B residue 2301 GLN Chi-restraints excluded: chain B residue 2304 LEU Chi-restraints excluded: chain B residue 2521 ASN Chi-restraints excluded: chain B residue 2564 ASN Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain K residue 27 LYS Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 0.0870 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2564 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5068 Z= 0.187 Angle : 0.586 10.752 6872 Z= 0.295 Chirality : 0.042 0.142 788 Planarity : 0.005 0.049 902 Dihedral : 5.342 81.841 690 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.21 % Allowed : 19.81 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.33), residues: 630 helix: 0.28 (0.33), residues: 249 sheet: -2.25 (0.87), residues: 37 loop : -1.40 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B2565 HIS 0.002 0.001 HIS B2020 PHE 0.017 0.002 PHE B2693 TYR 0.029 0.002 TYR B2576 ARG 0.004 0.000 ARG B2676 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: B 2666 SER cc_start: 0.8099 (p) cc_final: 0.7860 (p) outliers start: 17 outliers final: 16 residues processed: 101 average time/residue: 0.1688 time to fit residues: 22.0316 Evaluate side-chains 111 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2052 ASP Chi-restraints excluded: chain B residue 2248 ARG Chi-restraints excluded: chain B residue 2261 ASN Chi-restraints excluded: chain B residue 2301 GLN Chi-restraints excluded: chain B residue 2304 LEU Chi-restraints excluded: chain B residue 2521 ASN Chi-restraints excluded: chain B residue 2564 ASN Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2674 ASP Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain K residue 27 LYS Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.0060 chunk 15 optimal weight: 0.0980 chunk 46 optimal weight: 0.0970 chunk 7 optimal weight: 0.3980 overall best weight: 0.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5068 Z= 0.145 Angle : 0.575 12.392 6872 Z= 0.286 Chirality : 0.042 0.206 788 Planarity : 0.005 0.048 902 Dihedral : 5.111 73.570 690 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.83 % Allowed : 20.38 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.33), residues: 630 helix: 0.36 (0.34), residues: 251 sheet: -2.16 (0.88), residues: 37 loop : -1.37 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B2565 HIS 0.002 0.001 HIS B2553 PHE 0.018 0.001 PHE B2693 TYR 0.019 0.002 TYR B2576 ARG 0.003 0.000 ARG B2227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: B 2666 SER cc_start: 0.8050 (p) cc_final: 0.7827 (p) outliers start: 15 outliers final: 13 residues processed: 100 average time/residue: 0.1696 time to fit residues: 21.9786 Evaluate side-chains 108 residues out of total 575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2052 ASP Chi-restraints excluded: chain B residue 2248 ARG Chi-restraints excluded: chain B residue 2261 ASN Chi-restraints excluded: chain B residue 2304 LEU Chi-restraints excluded: chain B residue 2521 ASN Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2674 ASP Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain K residue 27 LYS Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 51 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.130995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.114180 restraints weight = 11025.408| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.50 r_work: 0.3582 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5068 Z= 0.181 Angle : 0.595 12.189 6872 Z= 0.297 Chirality : 0.042 0.197 788 Planarity : 0.005 0.049 902 Dihedral : 4.956 61.297 690 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 3.02 % Allowed : 20.94 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.33), residues: 630 helix: 0.36 (0.34), residues: 249 sheet: -2.20 (0.87), residues: 37 loop : -1.45 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B2565 HIS 0.002 0.001 HIS B2553 PHE 0.017 0.001 PHE B2693 TYR 0.017 0.002 TYR B2576 ARG 0.003 0.000 ARG B2676 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1827.87 seconds wall clock time: 33 minutes 34.99 seconds (2014.99 seconds total)