Starting phenix.real_space_refine on Mon Sep 23 16:46:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j97_36090/09_2024/8j97_36090.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j97_36090/09_2024/8j97_36090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j97_36090/09_2024/8j97_36090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j97_36090/09_2024/8j97_36090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j97_36090/09_2024/8j97_36090.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j97_36090/09_2024/8j97_36090.cif" } resolution = 3.2 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= 0.000 sd= 0.011 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 13 5.16 5 C 2466 2.51 5 N 649 2.21 5 O 731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3863 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2196 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 289} Chain breaks: 6 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 182 Chain: "H" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 864 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "L" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 729 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "V" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 2.92, per 1000 atoms: 0.76 Number of scatterers: 3863 At special positions: 0 Unit cell: (55.2967, 103.85, 83.6194, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 P 4 15.00 O 731 8.00 N 649 7.00 C 2466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.84 Conformation dependent library (CDL) restraints added in 411.5 milliseconds 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 12 sheets defined 6.6% alpha, 51.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.977A pdb=" N ARG A 282 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 80 removed outlier: 3.792A pdb=" N ASN H 80 " --> pdb=" O THR H 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 77 through 80' Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.026A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 118 removed outlier: 3.530A pdb=" N PHE A 117 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 7.304A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 55 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLN A 85 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU A 57 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASN A 83 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N CYS A 59 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL A 81 " --> pdb=" O CYS A 59 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE A 61 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A 79 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 28 removed outlier: 7.304A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 188 removed outlier: 3.557A pdb=" N ARG A 188 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 197 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 188 removed outlier: 3.557A pdb=" N ARG A 188 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 197 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 208 removed outlier: 4.076A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER A 330 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL A 228 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.544A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 60 through 63 removed outlier: 3.555A pdb=" N TYR H 60 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 60 through 63 removed outlier: 3.555A pdb=" N TYR H 60 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 7 through 8 Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.282A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.282A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 183 hydrogen bonds defined for protein. 465 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: 1.53 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 627 1.32 - 1.44: 1050 1.44 - 1.56: 2239 1.56 - 1.69: 11 1.69 - 1.81: 17 Bond restraints: 3944 Sorted by residual: bond pdb=" OG1 TPO V 307 " pdb=" P TPO V 307 " ideal model delta sigma weight residual 1.717 1.599 0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" OG1 TPO V 310 " pdb=" P TPO V 310 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" O1P SEP V 311 " pdb=" P SEP V 311 " ideal model delta sigma weight residual 1.610 1.513 0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" O2P SEP V 311 " pdb=" P SEP V 311 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" O3P SEP V 311 " pdb=" P SEP V 311 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.24e+01 ... (remaining 3939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 5322 2.88 - 5.75: 73 5.75 - 8.63: 12 8.63 - 11.51: 5 11.51 - 14.38: 2 Bond angle restraints: 5414 Sorted by residual: angle pdb=" C ASP A 342 " pdb=" N VAL A 343 " pdb=" CA VAL A 343 " ideal model delta sigma weight residual 121.97 129.37 -7.40 1.00e+00 1.00e+00 5.48e+01 angle pdb=" CA PHE A 115 " pdb=" CB PHE A 115 " pdb=" CG PHE A 115 " ideal model delta sigma weight residual 113.80 121.12 -7.32 1.00e+00 1.00e+00 5.35e+01 angle pdb=" C PRO A 114 " pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " ideal model delta sigma weight residual 111.56 101.98 9.58 1.65e+00 3.67e-01 3.37e+01 angle pdb=" N VAL A 343 " pdb=" CA VAL A 343 " pdb=" CB VAL A 343 " ideal model delta sigma weight residual 109.84 116.68 -6.84 1.32e+00 5.74e-01 2.68e+01 angle pdb=" CB TPO V 307 " pdb=" OG1 TPO V 307 " pdb=" P TPO V 307 " ideal model delta sigma weight residual 119.31 104.93 14.38 3.00e+00 1.11e-01 2.30e+01 ... (remaining 5409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2140 17.85 - 35.70: 136 35.70 - 53.55: 29 53.55 - 71.40: 1 71.40 - 89.25: 5 Dihedral angle restraints: 2311 sinusoidal: 732 harmonic: 1579 Sorted by residual: dihedral pdb=" CA LYS A 229 " pdb=" C LYS A 229 " pdb=" N LYS A 230 " pdb=" CA LYS A 230 " ideal model delta harmonic sigma weight residual -180.00 -154.20 -25.80 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA ASP A 342 " pdb=" C ASP A 342 " pdb=" N VAL A 343 " pdb=" CA VAL A 343 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLN L 90 " pdb=" C GLN L 90 " pdb=" N GLN L 91 " pdb=" CA GLN L 91 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 2308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 456 0.046 - 0.091: 140 0.091 - 0.137: 48 0.137 - 0.183: 5 0.183 - 0.228: 1 Chirality restraints: 650 Sorted by residual: chirality pdb=" CB VAL A 343 " pdb=" CA VAL A 343 " pdb=" CG1 VAL A 343 " pdb=" CG2 VAL A 343 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA TYR A 113 " pdb=" N TYR A 113 " pdb=" C TYR A 113 " pdb=" CB TYR A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA ILE A 318 " pdb=" N ILE A 318 " pdb=" C ILE A 318 " pdb=" CB ILE A 318 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 647 not shown) Planarity restraints: 692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 115 " -0.024 2.00e-02 2.50e+03 1.77e-02 5.46e+00 pdb=" CG PHE A 115 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 115 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 115 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 115 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 115 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 115 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 353 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 354 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 354 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 354 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 181 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 182 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 182 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 182 " 0.022 5.00e-02 4.00e+02 ... (remaining 689 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 948 2.79 - 3.32: 3377 3.32 - 3.85: 6084 3.85 - 4.37: 6966 4.37 - 4.90: 12439 Nonbonded interactions: 29814 Sorted by model distance: nonbonded pdb=" O ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.266 3.040 nonbonded pdb=" NH2 ARG A 7 " pdb=" OG SEP V 309 " model vdw 2.314 3.120 nonbonded pdb=" O THR A 221 " pdb=" OG1 THR A 221 " model vdw 2.326 3.040 nonbonded pdb=" NH2 ARG A 25 " pdb=" O VAL A 167 " model vdw 2.331 3.120 nonbonded pdb=" OD1 ASN H 31 " pdb=" N VAL H 32 " model vdw 2.347 3.120 ... (remaining 29809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.140 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 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 : 0.007 0.118 3944 Z= 0.448 Angle : 0.915 14.385 5414 Z= 0.483 Chirality : 0.050 0.228 650 Planarity : 0.006 0.053 692 Dihedral : 13.201 89.250 1285 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.28 % Allowed : 10.42 % Favored : 89.30 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % 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: -1.02 (0.37), residues: 517 helix: -1.09 (1.28), residues: 18 sheet: -0.98 (0.34), residues: 237 loop : -0.15 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP H 113 HIS 0.003 0.001 HIS A 353 PHE 0.039 0.003 PHE A 115 TYR 0.022 0.002 TYR A 21 ARG 0.004 0.001 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.406 Fit side-chains REVERT: A 169 ARG cc_start: 0.7855 (mtp180) cc_final: 0.7611 (mtm180) REVERT: H 33 TYR cc_start: 0.7978 (m-80) cc_final: 0.7644 (m-80) REVERT: H 86 MET cc_start: 0.7488 (mtt) cc_final: 0.7278 (mtm) outliers start: 1 outliers final: 1 residues processed: 89 average time/residue: 0.1574 time to fit residues: 17.4062 Evaluate side-chains 88 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.0970 chunk 39 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 26 optimal weight: 0.0870 chunk 40 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 overall best weight: 0.1334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3944 Z= 0.168 Angle : 0.627 10.792 5414 Z= 0.320 Chirality : 0.046 0.176 650 Planarity : 0.005 0.037 692 Dihedral : 5.631 45.674 582 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.97 % Allowed : 11.55 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.39), residues: 517 helix: -0.76 (1.06), residues: 24 sheet: -0.46 (0.34), residues: 250 loop : 0.13 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 113 HIS 0.001 0.000 HIS H 38 PHE 0.014 0.002 PHE A 115 TYR 0.021 0.001 TYR A 21 ARG 0.003 0.000 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.422 Fit side-chains REVERT: A 122 ASN cc_start: 0.7895 (t0) cc_final: 0.7308 (m-40) REVERT: A 169 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7579 (mtm180) REVERT: H 9 GLU cc_start: 0.7317 (mp0) cc_final: 0.6986 (mp0) REVERT: H 70 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7491 (mtm180) REVERT: H 86 MET cc_start: 0.7410 (mtt) cc_final: 0.7208 (mtm) outliers start: 7 outliers final: 5 residues processed: 90 average time/residue: 0.1855 time to fit residues: 20.0789 Evaluate side-chains 91 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.0070 chunk 13 optimal weight: 0.0370 chunk 47 optimal weight: 0.0270 chunk 51 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 0.0670 chunk 35 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 overall best weight: 0.1872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3944 Z= 0.160 Angle : 0.563 9.877 5414 Z= 0.287 Chirality : 0.045 0.160 650 Planarity : 0.004 0.036 692 Dihedral : 5.068 39.177 582 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.10 % Allowed : 11.55 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.39), residues: 517 helix: -0.26 (1.08), residues: 24 sheet: -0.25 (0.34), residues: 256 loop : 0.26 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 113 HIS 0.002 0.001 HIS H 38 PHE 0.008 0.002 PHE A 61 TYR 0.017 0.001 TYR A 21 ARG 0.002 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: H 70 ARG cc_start: 0.7956 (mtm110) cc_final: 0.7468 (mtm180) outliers start: 11 outliers final: 11 residues processed: 96 average time/residue: 0.1563 time to fit residues: 18.4684 Evaluate side-chains 100 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3944 Z= 0.414 Angle : 0.718 9.824 5414 Z= 0.369 Chirality : 0.049 0.182 650 Planarity : 0.006 0.055 692 Dihedral : 6.080 42.139 582 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.23 % Allowed : 12.96 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.38), residues: 517 helix: -0.78 (1.03), residues: 24 sheet: -0.31 (0.34), residues: 252 loop : -0.10 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 113 HIS 0.004 0.001 HIS A 210 PHE 0.018 0.003 PHE H 105 TYR 0.031 0.003 TYR A 21 ARG 0.005 0.001 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 122 ASN cc_start: 0.8125 (t0) cc_final: 0.7772 (t0) REVERT: A 255 MET cc_start: 0.6568 (tpp) cc_final: 0.5702 (tpp) REVERT: A 347 LEU cc_start: 0.8023 (mp) cc_final: 0.7787 (mp) REVERT: L 7 GLN cc_start: 0.7420 (tt0) cc_final: 0.7168 (mt0) outliers start: 15 outliers final: 13 residues processed: 94 average time/residue: 0.1595 time to fit residues: 18.8656 Evaluate side-chains 101 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 45 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3944 Z= 0.305 Angle : 0.648 9.368 5414 Z= 0.332 Chirality : 0.047 0.156 650 Planarity : 0.005 0.051 692 Dihedral : 5.793 38.290 581 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.38 % Allowed : 14.93 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.39), residues: 517 helix: -0.55 (1.08), residues: 24 sheet: -0.24 (0.34), residues: 252 loop : -0.14 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 113 HIS 0.003 0.001 HIS A 111 PHE 0.015 0.002 PHE H 105 TYR 0.025 0.002 TYR A 21 ARG 0.004 0.001 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 122 ASN cc_start: 0.8020 (t0) cc_final: 0.7693 (t0) REVERT: A 255 MET cc_start: 0.6511 (tpp) cc_final: 0.5619 (tpp) REVERT: A 347 LEU cc_start: 0.7992 (mp) cc_final: 0.7781 (mp) REVERT: L 7 GLN cc_start: 0.7410 (tt0) cc_final: 0.7156 (mt0) outliers start: 12 outliers final: 10 residues processed: 94 average time/residue: 0.1480 time to fit residues: 17.4568 Evaluate side-chains 99 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 41 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.0270 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3944 Z= 0.209 Angle : 0.597 9.035 5414 Z= 0.304 Chirality : 0.046 0.150 650 Planarity : 0.005 0.043 692 Dihedral : 5.395 37.453 581 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.82 % Allowed : 16.06 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.39), residues: 517 helix: -0.29 (1.08), residues: 24 sheet: -0.09 (0.34), residues: 253 loop : -0.00 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 113 HIS 0.002 0.001 HIS A 353 PHE 0.011 0.002 PHE H 105 TYR 0.019 0.001 TYR A 21 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 122 ASN cc_start: 0.8039 (t0) cc_final: 0.7755 (t0) REVERT: A 255 MET cc_start: 0.6540 (tpp) cc_final: 0.5667 (tpp) REVERT: L 7 GLN cc_start: 0.7405 (tt0) cc_final: 0.7190 (mt0) outliers start: 10 outliers final: 9 residues processed: 98 average time/residue: 0.1213 time to fit residues: 14.8630 Evaluate side-chains 100 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 0.0970 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3944 Z= 0.337 Angle : 0.669 8.984 5414 Z= 0.347 Chirality : 0.048 0.180 650 Planarity : 0.006 0.051 692 Dihedral : 5.735 37.529 581 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.66 % Allowed : 17.18 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.39), residues: 517 helix: -0.65 (1.09), residues: 24 sheet: -0.14 (0.34), residues: 252 loop : -0.18 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 113 HIS 0.003 0.001 HIS A 295 PHE 0.016 0.002 PHE H 105 TYR 0.026 0.002 TYR A 21 ARG 0.004 0.001 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 122 ASN cc_start: 0.8064 (t0) cc_final: 0.7747 (t0) REVERT: A 255 MET cc_start: 0.6528 (tpp) cc_final: 0.6258 (tpp) REVERT: L 7 GLN cc_start: 0.7433 (tt0) cc_final: 0.7214 (mt0) outliers start: 13 outliers final: 13 residues processed: 97 average time/residue: 0.1388 time to fit residues: 17.1774 Evaluate side-chains 106 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 43 optimal weight: 0.0020 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3944 Z= 0.258 Angle : 0.631 8.976 5414 Z= 0.325 Chirality : 0.047 0.178 650 Planarity : 0.005 0.048 692 Dihedral : 5.546 37.191 581 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.38 % Allowed : 19.15 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.39), residues: 517 helix: -0.62 (1.09), residues: 24 sheet: -0.16 (0.34), residues: 252 loop : -0.16 (0.43), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 113 HIS 0.003 0.001 HIS A 353 PHE 0.019 0.002 PHE A 277 TYR 0.021 0.002 TYR A 21 ARG 0.003 0.001 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 122 ASN cc_start: 0.8055 (t0) cc_final: 0.7775 (t0) REVERT: A 255 MET cc_start: 0.6542 (tpp) cc_final: 0.6265 (tpp) REVERT: L 7 GLN cc_start: 0.7452 (tt0) cc_final: 0.7236 (mt0) outliers start: 12 outliers final: 12 residues processed: 96 average time/residue: 0.1417 time to fit residues: 17.2088 Evaluate side-chains 103 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 46 optimal weight: 0.0980 chunk 30 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.0870 chunk 47 optimal weight: 0.4980 chunk 41 optimal weight: 0.0970 chunk 4 optimal weight: 0.0040 overall best weight: 0.1368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3944 Z= 0.151 Angle : 0.566 8.390 5414 Z= 0.287 Chirality : 0.045 0.157 650 Planarity : 0.005 0.038 692 Dihedral : 4.866 28.888 581 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.54 % Allowed : 20.28 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.39), residues: 517 helix: -0.27 (1.13), residues: 24 sheet: -0.05 (0.33), residues: 256 loop : -0.03 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 113 HIS 0.002 0.001 HIS A 353 PHE 0.036 0.002 PHE A 61 TYR 0.014 0.001 TYR A 21 ARG 0.002 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.7896 (t0) cc_final: 0.7653 (t0) REVERT: L 5 MET cc_start: 0.8504 (mmm) cc_final: 0.8212 (mmt) outliers start: 9 outliers final: 8 residues processed: 96 average time/residue: 0.1634 time to fit residues: 19.5328 Evaluate side-chains 96 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain L residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.0770 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3944 Z= 0.340 Angle : 0.692 8.971 5414 Z= 0.352 Chirality : 0.049 0.196 650 Planarity : 0.005 0.051 692 Dihedral : 5.617 35.829 581 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.38 % Allowed : 20.28 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.39), residues: 517 helix: -0.58 (1.10), residues: 24 sheet: -0.04 (0.34), residues: 252 loop : -0.13 (0.43), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 113 HIS 0.004 0.001 HIS H 38 PHE 0.016 0.002 PHE H 105 TYR 0.027 0.002 TYR A 21 ARG 0.005 0.001 ARG A 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 122 ASN cc_start: 0.8055 (t0) cc_final: 0.7770 (t0) REVERT: L 7 GLN cc_start: 0.7501 (tt0) cc_final: 0.7297 (mt0) outliers start: 12 outliers final: 9 residues processed: 92 average time/residue: 0.1442 time to fit residues: 16.7049 Evaluate side-chains 96 residues out of total 472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 0.0370 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 0.0970 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 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 = 0.3944 r_free = 0.3944 target = 0.142300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.131711 restraints weight = 5575.917| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.89 r_work: 0.3737 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3944 Z= 0.267 Angle : 0.647 9.328 5414 Z= 0.330 Chirality : 0.047 0.167 650 Planarity : 0.005 0.049 692 Dihedral : 5.503 35.293 581 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.97 % Allowed : 20.28 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.39), residues: 517 helix: -0.56 (1.09), residues: 24 sheet: -0.18 (0.34), residues: 255 loop : -0.22 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 113 HIS 0.004 0.001 HIS H 38 PHE 0.019 0.002 PHE A 277 TYR 0.021 0.002 TYR A 21 ARG 0.004 0.001 ARG H 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1405.15 seconds wall clock time: 28 minutes 51.32 seconds (1731.32 seconds total)