Starting phenix.real_space_refine on Tue Feb 11 12:03:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mjs_23883/02_2025/7mjs_23883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mjs_23883/02_2025/7mjs_23883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mjs_23883/02_2025/7mjs_23883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mjs_23883/02_2025/7mjs_23883.map" model { file = "/net/cci-nas-00/data/ceres_data/7mjs_23883/02_2025/7mjs_23883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mjs_23883/02_2025/7mjs_23883.cif" } resolution = 3.03 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= 0.022 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 1 5.49 5 S 26 5.16 5 C 3618 2.51 5 N 878 2.21 5 O 1013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5536 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1018 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain: "L" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 863 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "X" Number of atoms: 3592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3592 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'ZGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.57, per 1000 atoms: 0.83 Number of scatterers: 5536 At special positions: 0 Unit cell: (69.72, 69.72, 131.14, 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 26 16.00 P 1 15.00 O 1013 8.00 N 878 7.00 C 3618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, 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=2.03 Simple disulfide: pdb=" SG CYS X 207 " - pdb=" SG CYS X 460 " distance=2.03 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 Links applied NAG-ASN " NAG X 602 " - " ASN X 227 " " NAG X 603 " - " ASN X 218 " Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 795.2 milliseconds 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 54.8% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'X' and resid 37 through 42 removed outlier: 3.526A pdb=" N LEU X 42 " --> pdb=" O VAL X 38 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 47 removed outlier: 3.594A pdb=" N VAL X 46 " --> pdb=" O LEU X 42 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY X 47 " --> pdb=" O CYS X 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 42 through 47' Processing helix chain 'X' and resid 47 through 69 removed outlier: 4.666A pdb=" N TYR X 51 " --> pdb=" O GLY X 47 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN X 52 " --> pdb=" O GLY X 48 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLN X 63 " --> pdb=" O GLY X 59 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE X 64 " --> pdb=" O PHE X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 99 removed outlier: 3.630A pdb=" N ASP X 92 " --> pdb=" O ASP X 88 " (cutoff:3.500A) Proline residue: X 93 - end of helix Processing helix chain 'X' and resid 110 through 127 removed outlier: 3.884A pdb=" N ILE X 114 " --> pdb=" O LEU X 110 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR X 118 " --> pdb=" O ILE X 114 " (cutoff:3.500A) Proline residue: X 119 - end of helix Processing helix chain 'X' and resid 137 through 162 removed outlier: 3.534A pdb=" N TRP X 141 " --> pdb=" O GLY X 137 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR X 142 " --> pdb=" O GLN X 138 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE X 145 " --> pdb=" O TRP X 141 " (cutoff:3.500A) Proline residue: X 159 - end of helix Processing helix chain 'X' and resid 163 through 168 removed outlier: 4.385A pdb=" N SER X 168 " --> pdb=" O THR X 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 170 through 202 removed outlier: 3.599A pdb=" N VAL X 200 " --> pdb=" O GLN X 196 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS X 202 " --> pdb=" O GLN X 198 " (cutoff:3.500A) Processing helix chain 'X' and resid 218 through 223 removed outlier: 4.088A pdb=" N ALA X 222 " --> pdb=" O ASN X 218 " (cutoff:3.500A) Processing helix chain 'X' and resid 228 through 264 Processing helix chain 'X' and resid 281 through 289 removed outlier: 3.673A pdb=" N MET X 289 " --> pdb=" O LEU X 285 " (cutoff:3.500A) Processing helix chain 'X' and resid 291 through 322 removed outlier: 4.163A pdb=" N THR X 320 " --> pdb=" O ALA X 316 " (cutoff:3.500A) Processing helix chain 'X' and resid 328 through 354 Proline residue: X 345 - end of helix Processing helix chain 'X' and resid 355 through 366 removed outlier: 3.973A pdb=" N TYR X 361 " --> pdb=" O LYS X 357 " (cutoff:3.500A) Processing helix chain 'X' and resid 366 through 377 removed outlier: 4.321A pdb=" N PHE X 370 " --> pdb=" O SER X 366 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL X 375 " --> pdb=" O LEU X 371 " (cutoff:3.500A) Processing helix chain 'X' and resid 380 through 417 removed outlier: 3.620A pdb=" N TYR X 385 " --> pdb=" O LEU X 381 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE X 386 " --> pdb=" O VAL X 382 " (cutoff:3.500A) Proline residue: X 402 - end of helix Proline residue: X 407 - end of helix Processing helix chain 'X' and resid 425 through 453 removed outlier: 3.628A pdb=" N THR X 438 " --> pdb=" O PHE X 434 " (cutoff:3.500A) Processing helix chain 'X' and resid 463 through 473 Processing helix chain 'X' and resid 475 through 489 Processing helix chain 'X' and resid 490 through 492 No H-bonds generated for 'chain 'X' and resid 490 through 492' Processing helix chain 'X' and resid 497 through 505 removed outlier: 4.238A pdb=" N GLU X 501 " --> pdb=" O GLU X 497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.621A pdb=" N SER H 102 " --> pdb=" O SER H 36 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR H 60 " --> pdb=" O TYR H 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 13 through 15 removed outlier: 6.781A pdb=" N CYS H 99 " --> pdb=" O TRP H 122 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TRP H 122 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG H 101 " --> pdb=" O ASP H 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.368A pdb=" N LEU L 12 " --> pdb=" O GLU L 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55 removed outlier: 5.739A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 969 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: 1.69 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 836 1.31 - 1.44: 1687 1.44 - 1.56: 3112 1.56 - 1.69: 3 1.69 - 1.82: 39 Bond restraints: 5677 Sorted by residual: bond pdb=" C18 ZGS X 601 " pdb=" O20 ZGS X 601 " ideal model delta sigma weight residual 1.345 1.416 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" N VAL X 226 " pdb=" CA VAL X 226 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.19e-02 7.06e+03 1.22e+01 bond pdb=" C32 ZGS X 601 " pdb=" N31 ZGS X 601 " ideal model delta sigma weight residual 1.500 1.441 0.059 2.00e-02 2.50e+03 8.73e+00 bond pdb=" N ASN X 227 " pdb=" CA ASN X 227 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.22e-02 6.72e+03 7.72e+00 bond pdb=" N THR X 217 " pdb=" CA THR X 217 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.32e-02 5.74e+03 7.24e+00 ... (remaining 5672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 7623 2.57 - 5.14: 79 5.14 - 7.71: 15 7.71 - 10.28: 2 10.28 - 12.85: 1 Bond angle restraints: 7720 Sorted by residual: angle pdb=" N CYS X 460 " pdb=" CA CYS X 460 " pdb=" C CYS X 460 " ideal model delta sigma weight residual 114.31 108.51 5.80 1.29e+00 6.01e-01 2.02e+01 angle pdb=" O26 ZGS X 601 " pdb=" P25 ZGS X 601 " pdb=" O27 ZGS X 601 " ideal model delta sigma weight residual 121.97 109.12 12.85 3.00e+00 1.11e-01 1.83e+01 angle pdb=" N PHE X 219 " pdb=" CA PHE X 219 " pdb=" C PHE X 219 " ideal model delta sigma weight residual 113.23 108.29 4.94 1.24e+00 6.50e-01 1.59e+01 angle pdb=" C THR X 217 " pdb=" CA THR X 217 " pdb=" CB THR X 217 " ideal model delta sigma weight residual 111.06 117.68 -6.62 1.89e+00 2.80e-01 1.23e+01 angle pdb=" C VAL H 15 " pdb=" N GLN H 16 " pdb=" CA GLN H 16 " ideal model delta sigma weight residual 120.97 111.17 9.80 2.84e+00 1.24e-01 1.19e+01 ... (remaining 7715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3001 17.64 - 35.28: 264 35.28 - 52.91: 45 52.91 - 70.55: 14 70.55 - 88.19: 3 Dihedral angle restraints: 3327 sinusoidal: 1289 harmonic: 2038 Sorted by residual: dihedral pdb=" CB CYS X 207 " pdb=" SG CYS X 207 " pdb=" SG CYS X 460 " pdb=" CB CYS X 460 " ideal model delta sinusoidal sigma weight residual -86.00 -31.66 -54.34 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CA ASN L 96 " pdb=" C ASN L 96 " pdb=" N GLN L 97 " pdb=" CA GLN L 97 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" C THR X 217 " pdb=" N THR X 217 " pdb=" CA THR X 217 " pdb=" CB THR X 217 " ideal model delta harmonic sigma weight residual -122.00 -131.98 9.98 0 2.50e+00 1.60e-01 1.59e+01 ... (remaining 3324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 881 0.198 - 0.396: 3 0.396 - 0.595: 0 0.595 - 0.793: 0 0.793 - 0.991: 1 Chirality restraints: 885 Sorted by residual: chirality pdb=" C1 NAG X 603 " pdb=" ND2 ASN X 218 " pdb=" C2 NAG X 603 " pdb=" O5 NAG X 603 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" C1 NAG X 602 " pdb=" ND2 ASN X 227 " pdb=" C2 NAG X 602 " pdb=" O5 NAG X 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA THR X 217 " pdb=" N THR X 217 " pdb=" C THR X 217 " pdb=" CB THR X 217 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 882 not shown) Planarity restraints: 953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 602 " -0.114 2.00e-02 2.50e+03 9.38e-02 1.10e+02 pdb=" C7 NAG X 602 " 0.033 2.00e-02 2.50e+03 pdb=" C8 NAG X 602 " -0.086 2.00e-02 2.50e+03 pdb=" N2 NAG X 602 " 0.150 2.00e-02 2.50e+03 pdb=" O7 NAG X 602 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 603 " 0.091 2.00e-02 2.50e+03 7.74e-02 7.48e+01 pdb=" C7 NAG X 603 " -0.015 2.00e-02 2.50e+03 pdb=" C8 NAG X 603 " -0.023 2.00e-02 2.50e+03 pdb=" N2 NAG X 603 " -0.125 2.00e-02 2.50e+03 pdb=" O7 NAG X 603 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA L 44 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.45e+00 pdb=" N PRO L 45 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO L 45 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 45 " 0.022 5.00e-02 4.00e+02 ... (remaining 950 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 999 2.76 - 3.30: 5470 3.30 - 3.83: 9160 3.83 - 4.37: 11223 4.37 - 4.90: 19596 Nonbonded interactions: 46448 Sorted by model distance: nonbonded pdb=" O SER H 66 " pdb=" NH1 ARG H 70 " model vdw 2.228 3.120 nonbonded pdb=" OG SER H 58 " pdb=" O PHE X 213 " model vdw 2.247 3.040 nonbonded pdb=" O GLY X 363 " pdb=" OG SER X 366 " model vdw 2.287 3.040 nonbonded pdb=" NH1 ARG H 41 " pdb=" OD1 ASP H 93 " model vdw 2.304 3.120 nonbonded pdb=" OH TYR H 105 " pdb=" OG SER L 92 " model vdw 2.333 3.040 ... (remaining 46443 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: 2.880 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.840 Find NCS groups from input model: 0.060 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.005 0.071 5677 Z= 0.334 Angle : 0.756 12.847 7720 Z= 0.424 Chirality : 0.057 0.991 885 Planarity : 0.006 0.094 951 Dihedral : 14.033 88.191 2018 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Cbeta Deviations : 0.15 % 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: -3.02 (0.26), residues: 695 helix: -1.42 (0.23), residues: 341 sheet: -2.47 (0.41), residues: 114 loop : -2.35 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 349 HIS 0.003 0.001 HIS X 291 PHE 0.015 0.002 PHE X 318 TYR 0.014 0.001 TYR X 146 ARG 0.002 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.609 Fit side-chains REVERT: H 46 LYS cc_start: 0.8527 (mttp) cc_final: 0.8312 (mttp) REVERT: H 49 GLU cc_start: 0.7553 (tt0) cc_final: 0.7207 (tt0) REVERT: L 46 LYS cc_start: 0.8591 (mttt) cc_final: 0.8258 (mttp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1736 time to fit residues: 25.7161 Evaluate side-chains 93 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.0370 chunk 54 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN H 112 GLN L 38 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 240 ASN X 290 ASN X 291 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.125124 restraints weight = 6973.752| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.94 r_work: 0.3409 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5677 Z= 0.196 Angle : 0.554 7.980 7720 Z= 0.292 Chirality : 0.043 0.296 885 Planarity : 0.004 0.040 951 Dihedral : 6.439 59.030 839 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.01 % Allowed : 10.81 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.30), residues: 695 helix: 0.10 (0.27), residues: 345 sheet: -1.90 (0.44), residues: 103 loop : -1.69 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 349 HIS 0.006 0.001 HIS X 291 PHE 0.015 0.001 PHE X 318 TYR 0.015 0.001 TYR X 492 ARG 0.002 0.000 ARG H 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.637 Fit side-chains REVERT: H 49 GLU cc_start: 0.8238 (tt0) cc_final: 0.8031 (tt0) REVERT: L 46 LYS cc_start: 0.8992 (mttt) cc_final: 0.8699 (mttp) outliers start: 6 outliers final: 5 residues processed: 104 average time/residue: 0.1705 time to fit residues: 23.7622 Evaluate side-chains 97 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 429 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 0.0970 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.144617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.126367 restraints weight = 6955.307| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.04 r_work: 0.3421 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5677 Z= 0.179 Angle : 0.531 7.306 7720 Z= 0.277 Chirality : 0.042 0.248 885 Planarity : 0.004 0.044 951 Dihedral : 5.665 57.057 839 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.53 % Allowed : 11.99 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.31), residues: 695 helix: 0.68 (0.27), residues: 347 sheet: -1.57 (0.45), residues: 103 loop : -1.37 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 349 HIS 0.002 0.000 HIS H 38 PHE 0.015 0.001 PHE X 318 TYR 0.018 0.001 TYR H 33 ARG 0.001 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.595 Fit side-chains REVERT: L 46 LYS cc_start: 0.9034 (mttt) cc_final: 0.8712 (mttp) REVERT: X 170 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7302 (mm-30) REVERT: X 240 ASN cc_start: 0.8765 (m-40) cc_final: 0.8409 (m-40) outliers start: 15 outliers final: 11 residues processed: 110 average time/residue: 0.1534 time to fit residues: 22.8148 Evaluate side-chains 111 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 464 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 290 ASN X 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.144892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.126354 restraints weight = 7123.385| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.09 r_work: 0.3422 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5677 Z= 0.188 Angle : 0.534 7.032 7720 Z= 0.278 Chirality : 0.042 0.244 885 Planarity : 0.004 0.045 951 Dihedral : 5.432 54.971 839 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.70 % Allowed : 13.85 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.32), residues: 695 helix: 0.89 (0.28), residues: 351 sheet: -1.32 (0.45), residues: 103 loop : -1.27 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 349 HIS 0.002 0.001 HIS H 38 PHE 0.015 0.001 PHE X 318 TYR 0.028 0.001 TYR X 492 ARG 0.002 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.558 Fit side-chains REVERT: L 46 LYS cc_start: 0.9028 (mttt) cc_final: 0.8714 (mttp) REVERT: L 84 PHE cc_start: 0.7890 (m-10) cc_final: 0.7570 (m-10) REVERT: X 170 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7346 (mm-30) REVERT: X 240 ASN cc_start: 0.8786 (m-40) cc_final: 0.8412 (m-40) REVERT: X 314 ASN cc_start: 0.7482 (m-40) cc_final: 0.7111 (m-40) outliers start: 16 outliers final: 12 residues processed: 113 average time/residue: 0.1413 time to fit residues: 21.8922 Evaluate side-chains 111 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 464 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 19 optimal weight: 3.9990 chunk 42 optimal weight: 0.0170 chunk 54 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.125911 restraints weight = 7247.797| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.78 r_work: 0.3391 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5677 Z= 0.186 Angle : 0.534 7.203 7720 Z= 0.276 Chirality : 0.042 0.237 885 Planarity : 0.004 0.044 951 Dihedral : 5.274 53.727 839 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.55 % Allowed : 14.70 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.32), residues: 695 helix: 1.04 (0.28), residues: 351 sheet: -1.17 (0.46), residues: 103 loop : -1.13 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 PHE 0.014 0.001 PHE X 318 TYR 0.025 0.001 TYR X 492 ARG 0.003 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.562 Fit side-chains REVERT: L 46 LYS cc_start: 0.8959 (mttt) cc_final: 0.8662 (mttp) REVERT: X 240 ASN cc_start: 0.8727 (m-40) cc_final: 0.8365 (m-40) REVERT: X 314 ASN cc_start: 0.7289 (m-40) cc_final: 0.6970 (m-40) REVERT: X 473 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8421 (tp) outliers start: 21 outliers final: 15 residues processed: 116 average time/residue: 0.1448 time to fit residues: 23.1305 Evaluate side-chains 116 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 285 LEU Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 464 SER Chi-restraints excluded: chain X residue 473 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.141370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124459 restraints weight = 7200.130| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.85 r_work: 0.3371 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5677 Z= 0.219 Angle : 0.553 7.387 7720 Z= 0.286 Chirality : 0.043 0.238 885 Planarity : 0.004 0.044 951 Dihedral : 5.297 54.393 839 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.21 % Allowed : 15.03 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.32), residues: 695 helix: 1.01 (0.28), residues: 351 sheet: -1.09 (0.46), residues: 103 loop : -1.10 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 PHE 0.016 0.001 PHE X 318 TYR 0.040 0.002 TYR X 492 ARG 0.003 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.651 Fit side-chains REVERT: L 46 LYS cc_start: 0.8968 (mttt) cc_final: 0.8671 (mttp) REVERT: X 240 ASN cc_start: 0.8739 (m-40) cc_final: 0.8398 (m-40) REVERT: X 314 ASN cc_start: 0.7342 (m-40) cc_final: 0.7023 (m-40) REVERT: X 473 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8478 (tp) outliers start: 19 outliers final: 14 residues processed: 115 average time/residue: 0.1470 time to fit residues: 23.3205 Evaluate side-chains 115 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 288 VAL Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 464 SER Chi-restraints excluded: chain X residue 473 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 50 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 423 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.141123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124009 restraints weight = 7187.986| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.87 r_work: 0.3365 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5677 Z= 0.228 Angle : 0.562 7.082 7720 Z= 0.292 Chirality : 0.044 0.236 885 Planarity : 0.004 0.043 951 Dihedral : 5.353 54.672 839 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.38 % Allowed : 15.71 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.32), residues: 695 helix: 1.05 (0.28), residues: 351 sheet: -1.08 (0.46), residues: 103 loop : -1.10 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 PHE 0.015 0.001 PHE X 318 TYR 0.033 0.002 TYR X 492 ARG 0.003 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.593 Fit side-chains REVERT: L 46 LYS cc_start: 0.8979 (mttt) cc_final: 0.8674 (mttp) REVERT: X 240 ASN cc_start: 0.8742 (m-40) cc_final: 0.8385 (m-40) REVERT: X 314 ASN cc_start: 0.7408 (m-40) cc_final: 0.7073 (m-40) REVERT: X 473 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8433 (tp) outliers start: 20 outliers final: 17 residues processed: 113 average time/residue: 0.1474 time to fit residues: 22.8103 Evaluate side-chains 118 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 43 CYS Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 288 VAL Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 464 SER Chi-restraints excluded: chain X residue 473 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.141501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124439 restraints weight = 7228.810| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.88 r_work: 0.3370 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5677 Z= 0.221 Angle : 0.558 6.955 7720 Z= 0.290 Chirality : 0.043 0.232 885 Planarity : 0.004 0.043 951 Dihedral : 5.327 54.765 839 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.38 % Allowed : 15.88 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.32), residues: 695 helix: 1.15 (0.28), residues: 351 sheet: -1.01 (0.47), residues: 103 loop : -1.10 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 PHE 0.015 0.001 PHE X 318 TYR 0.032 0.002 TYR X 492 ARG 0.003 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.614 Fit side-chains REVERT: L 46 LYS cc_start: 0.8982 (mttt) cc_final: 0.8687 (mttp) REVERT: X 240 ASN cc_start: 0.8732 (m-40) cc_final: 0.8380 (m-40) REVERT: X 314 ASN cc_start: 0.7399 (m-40) cc_final: 0.7062 (m-40) REVERT: X 473 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8433 (tp) outliers start: 20 outliers final: 17 residues processed: 114 average time/residue: 0.1418 time to fit residues: 22.3624 Evaluate side-chains 120 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 43 CYS Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 288 VAL Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 464 SER Chi-restraints excluded: chain X residue 473 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.141129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124086 restraints weight = 7241.343| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.88 r_work: 0.3364 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5677 Z= 0.226 Angle : 0.569 7.444 7720 Z= 0.294 Chirality : 0.043 0.229 885 Planarity : 0.004 0.043 951 Dihedral : 5.343 54.834 839 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.38 % Allowed : 16.89 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.32), residues: 695 helix: 1.17 (0.28), residues: 357 sheet: -1.23 (0.44), residues: 116 loop : -1.01 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.001 PHE X 318 TYR 0.040 0.002 TYR X 492 ARG 0.003 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.559 Fit side-chains REVERT: L 46 LYS cc_start: 0.8990 (mttt) cc_final: 0.8686 (mttp) REVERT: X 240 ASN cc_start: 0.8734 (m-40) cc_final: 0.8376 (m-40) REVERT: X 314 ASN cc_start: 0.7404 (m-40) cc_final: 0.7061 (m-40) REVERT: X 473 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8434 (tp) outliers start: 20 outliers final: 17 residues processed: 113 average time/residue: 0.1433 time to fit residues: 22.1278 Evaluate side-chains 119 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 43 CYS Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 288 VAL Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 464 SER Chi-restraints excluded: chain X residue 473 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.0970 chunk 7 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.145466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127259 restraints weight = 6924.346| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.04 r_work: 0.3433 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5677 Z= 0.186 Angle : 0.559 7.983 7720 Z= 0.287 Chirality : 0.043 0.221 885 Planarity : 0.004 0.043 951 Dihedral : 5.245 53.977 839 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.87 % Allowed : 17.06 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.32), residues: 695 helix: 1.35 (0.28), residues: 357 sheet: -0.84 (0.48), residues: 103 loop : -1.03 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 PHE 0.014 0.001 PHE X 318 TYR 0.038 0.001 TYR X 492 ARG 0.004 0.000 ARG L 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.619 Fit side-chains REVERT: L 46 LYS cc_start: 0.9021 (mttt) cc_final: 0.8701 (mttp) REVERT: X 240 ASN cc_start: 0.8764 (m-40) cc_final: 0.8418 (m-40) REVERT: X 314 ASN cc_start: 0.7212 (m-40) cc_final: 0.6890 (m-40) REVERT: X 473 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8419 (tp) outliers start: 17 outliers final: 15 residues processed: 117 average time/residue: 0.1476 time to fit residues: 23.6889 Evaluate side-chains 119 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 109 ILE Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain X residue 43 CYS Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 230 HIS Chi-restraints excluded: chain X residue 288 VAL Chi-restraints excluded: chain X residue 429 SER Chi-restraints excluded: chain X residue 464 SER Chi-restraints excluded: chain X residue 473 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 59 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 16 optimal weight: 0.0070 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.145329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126827 restraints weight = 7002.995| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.08 r_work: 0.3425 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5677 Z= 0.201 Angle : 0.558 7.968 7720 Z= 0.287 Chirality : 0.043 0.219 885 Planarity : 0.004 0.043 951 Dihedral : 5.227 54.316 839 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.53 % Allowed : 18.41 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.32), residues: 695 helix: 1.39 (0.28), residues: 356 sheet: -0.83 (0.48), residues: 103 loop : -1.02 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 PHE 0.015 0.001 PHE X 318 TYR 0.038 0.001 TYR X 492 ARG 0.004 0.000 ARG L 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3101.62 seconds wall clock time: 55 minutes 48.08 seconds (3348.08 seconds total)