Starting phenix.real_space_refine on Fri Dec 27 12:43:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ey4_31377/12_2024/7ey4_31377.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ey4_31377/12_2024/7ey4_31377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ey4_31377/12_2024/7ey4_31377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ey4_31377/12_2024/7ey4_31377.map" model { file = "/net/cci-nas-00/data/ceres_data/7ey4_31377/12_2024/7ey4_31377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ey4_31377/12_2024/7ey4_31377.cif" } resolution = 3.69 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 3000 2.51 5 N 772 2.21 5 O 894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4683 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 985 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "N" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1359 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 7 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.49, per 1000 atoms: 0.96 Number of scatterers: 4683 At special positions: 0 Unit cell: (62.13, 80.66, 110.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 894 8.00 N 772 7.00 C 3000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS N 131 " - pdb=" SG CYS N 166 " distance=2.05 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 BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN N 165 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 559.6 milliseconds 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1072 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 11 sheets defined 7.2% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.648A pdb=" N ASP H 31 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.577A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 3.653A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.923A pdb=" N GLU L 70 " --> pdb=" O PHE L 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.193A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.513A pdb=" N SER H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP H 73 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA5, first strand: chain 'H' and resid 45 through 47 removed outlier: 4.277A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG H 98 " --> pdb=" O ASP H 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 49 through 50 removed outlier: 3.668A pdb=" N TYR H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 356 through 358 removed outlier: 3.687A pdb=" N ILE R 402 " --> pdb=" O TYR R 508 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL R 433 " --> pdb=" O LYS R 378 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS R 378 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'N' and resid 50 through 55 removed outlier: 3.774A pdb=" N ASP N 53 " --> pdb=" O ARG N 273 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP N 287 " --> pdb=" O LYS N 278 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 63 through 64 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 63 through 64 current: chain 'N' and resid 116 through 121 removed outlier: 4.174A pdb=" N ASN N 164 " --> pdb=" O GLU N 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 163 through 164 current: chain 'N' and resid 200 through 205 removed outlier: 5.953A pdb=" N SER N 205 " --> pdb=" O PRO N 225 " (cutoff:3.500A) 103 hydrogen bonds defined for protein. 252 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: 1.18 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1473 1.35 - 1.48: 1418 1.48 - 1.61: 1891 1.61 - 1.74: 0 1.74 - 1.88: 21 Bond restraints: 4803 Sorted by residual: bond pdb=" CA SER H 107 " pdb=" CB SER H 107 " ideal model delta sigma weight residual 1.532 1.464 0.067 1.82e-02 3.02e+03 1.37e+01 bond pdb=" N CYS N 166 " pdb=" CA CYS N 166 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.58e+00 bond pdb=" N PHE N 168 " pdb=" CA PHE N 168 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.22e-02 6.72e+03 7.54e+00 bond pdb=" CA SER H 104 " pdb=" CB SER H 104 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.22e-02 6.72e+03 7.34e+00 bond pdb=" N ASP H 105 " pdb=" CA ASP H 105 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.34e-02 5.57e+03 7.04e+00 ... (remaining 4798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 6374 2.63 - 5.25: 127 5.25 - 7.88: 15 7.88 - 10.50: 1 10.50 - 13.13: 2 Bond angle restraints: 6519 Sorted by residual: angle pdb=" N VAL L 29 " pdb=" CA VAL L 29 " pdb=" C VAL L 29 " ideal model delta sigma weight residual 111.90 107.22 4.68 8.10e-01 1.52e+00 3.34e+01 angle pdb=" CA CYS R 379 " pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 114.40 127.53 -13.13 2.30e+00 1.89e-01 3.26e+01 angle pdb=" CA CYS R 432 " pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 114.40 127.18 -12.78 2.30e+00 1.89e-01 3.09e+01 angle pdb=" N CYS R 379 " pdb=" CA CYS R 379 " pdb=" C CYS R 379 " ideal model delta sigma weight residual 108.38 114.13 -5.75 1.35e+00 5.49e-01 1.82e+01 angle pdb=" N CYS R 432 " pdb=" CA CYS R 432 " pdb=" C CYS R 432 " ideal model delta sigma weight residual 108.60 114.65 -6.05 1.46e+00 4.69e-01 1.71e+01 ... (remaining 6514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 2582 21.25 - 42.51: 184 42.51 - 63.76: 27 63.76 - 85.01: 13 85.01 - 106.26: 12 Dihedral angle restraints: 2818 sinusoidal: 1129 harmonic: 1689 Sorted by residual: dihedral pdb=" CA SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta harmonic sigma weight residual 180.00 132.41 47.59 0 5.00e+00 4.00e-02 9.06e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual -86.00 -10.28 -75.72 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CA CYS R 379 " pdb=" C CYS R 379 " pdb=" N TYR R 380 " pdb=" CA TYR R 380 " ideal model delta harmonic sigma weight residual -180.00 -140.32 -39.68 0 5.00e+00 4.00e-02 6.30e+01 ... (remaining 2815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 624 0.078 - 0.156: 70 0.156 - 0.233: 4 0.233 - 0.311: 2 0.311 - 0.389: 1 Chirality restraints: 701 Sorted by residual: chirality pdb=" C1 BMA A 3 " pdb=" O4 NAG A 2 " pdb=" C2 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.79e+02 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.58e+00 chirality pdb=" CA CYS R 432 " pdb=" N CYS R 432 " pdb=" C CYS R 432 " pdb=" CB CYS R 432 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 698 not shown) Planarity restraints: 836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.322 2.00e-02 2.50e+03 2.72e-01 9.26e+02 pdb=" C7 NAG A 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.471 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " -0.293 2.00e-02 2.50e+03 2.52e-01 7.94e+02 pdb=" C7 NAG A 2 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " 0.007 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " 0.430 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO L 8 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.035 5.00e-02 4.00e+02 ... (remaining 833 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 180 2.70 - 3.25: 4472 3.25 - 3.80: 6731 3.80 - 4.35: 8835 4.35 - 4.90: 15297 Nonbonded interactions: 35515 Sorted by model distance: nonbonded pdb=" OH TYR N 37 " pdb=" O LEU N 54 " model vdw 2.150 3.040 nonbonded pdb=" OD1 ASP N 40 " pdb=" OH TYR N 204 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR N 91 " pdb=" OE1 GLU N 191 " model vdw 2.217 3.040 nonbonded pdb=" NH2 ARG H 98 " pdb=" OD2 ASP H 117 " model vdw 2.237 3.120 nonbonded pdb=" NH2 ARG L 31 " pdb=" OE1 GLU R 340 " model vdw 2.241 3.120 ... (remaining 35510 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.690 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.230 Find NCS groups from input model: 0.050 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 0.068 4803 Z= 0.449 Angle : 0.901 13.127 6519 Z= 0.512 Chirality : 0.053 0.389 701 Planarity : 0.014 0.272 835 Dihedral : 16.811 106.261 1728 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.50 % Favored : 86.15 % Rotamer: Outliers : 0.20 % Allowed : 0.60 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.34), residues: 563 helix: -3.57 (0.84), residues: 20 sheet: -0.83 (0.39), residues: 181 loop : -2.14 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 436 HIS 0.001 0.001 HIS N 66 PHE 0.028 0.002 PHE H 56 TYR 0.024 0.002 TYR H 110 ARG 0.017 0.001 ARG N 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.597 Fit side-chains REVERT: H 74 ASP cc_start: 0.8334 (m-30) cc_final: 0.7991 (m-30) REVERT: N 54 LEU cc_start: 0.7149 (mp) cc_final: 0.6142 (mt) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.2304 time to fit residues: 34.8507 Evaluate side-chains 98 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.0040 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 ASN N 164 ASN N 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4803 Z= 0.230 Angle : 0.726 8.089 6519 Z= 0.378 Chirality : 0.048 0.276 701 Planarity : 0.005 0.057 835 Dihedral : 12.746 85.147 708 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.41 % Favored : 90.41 % Rotamer: Outliers : 1.00 % Allowed : 11.40 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.34), residues: 563 helix: -3.42 (0.95), residues: 20 sheet: -0.37 (0.39), residues: 192 loop : -2.01 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 436 HIS 0.000 0.000 HIS N 66 PHE 0.015 0.002 PHE N 43 TYR 0.015 0.001 TYR R 369 ARG 0.006 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.530 Fit side-chains REVERT: H 74 ASP cc_start: 0.8434 (m-30) cc_final: 0.8071 (m-30) REVERT: R 414 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7168 (mm-40) REVERT: N 64 TRP cc_start: 0.7477 (t60) cc_final: 0.7211 (t60) outliers start: 5 outliers final: 3 residues processed: 114 average time/residue: 0.2034 time to fit residues: 28.3982 Evaluate side-chains 92 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 130 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4803 Z= 0.248 Angle : 0.703 8.592 6519 Z= 0.361 Chirality : 0.047 0.224 701 Planarity : 0.005 0.087 835 Dihedral : 10.614 76.348 708 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.59 % Favored : 90.23 % Rotamer: Outliers : 2.80 % Allowed : 14.60 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.34), residues: 563 helix: -3.29 (0.98), residues: 20 sheet: -0.28 (0.39), residues: 188 loop : -1.95 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 436 HIS 0.001 0.001 HIS N 49 PHE 0.014 0.002 PHE H 56 TYR 0.015 0.001 TYR H 110 ARG 0.005 0.001 ARG N 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.504 Fit side-chains REVERT: H 74 ASP cc_start: 0.8462 (m-30) cc_final: 0.8035 (m-30) REVERT: N 64 TRP cc_start: 0.7691 (t60) cc_final: 0.7269 (t60) outliers start: 14 outliers final: 9 residues processed: 104 average time/residue: 0.2101 time to fit residues: 26.6722 Evaluate side-chains 91 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 0.0050 chunk 0 optimal weight: 2.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4803 Z= 0.326 Angle : 0.720 7.964 6519 Z= 0.373 Chirality : 0.047 0.254 701 Planarity : 0.006 0.092 835 Dihedral : 9.195 63.929 708 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.41 % Favored : 90.41 % Rotamer: Outliers : 5.00 % Allowed : 15.40 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.34), residues: 563 helix: -3.22 (0.93), residues: 20 sheet: -0.15 (0.40), residues: 186 loop : -2.01 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 436 HIS 0.001 0.001 HIS N 49 PHE 0.022 0.002 PHE H 56 TYR 0.017 0.001 TYR H 110 ARG 0.008 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: L 93 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7682 (m-40) REVERT: H 74 ASP cc_start: 0.8507 (m-30) cc_final: 0.8172 (m-30) REVERT: H 114 ASP cc_start: 0.9080 (t0) cc_final: 0.8836 (t0) REVERT: N 198 ASP cc_start: 0.7739 (t0) cc_final: 0.7539 (t0) outliers start: 25 outliers final: 15 residues processed: 113 average time/residue: 0.1972 time to fit residues: 27.4905 Evaluate side-chains 104 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4803 Z= 0.239 Angle : 0.677 8.278 6519 Z= 0.347 Chirality : 0.046 0.236 701 Planarity : 0.005 0.083 835 Dihedral : 8.001 51.827 708 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 4.00 % Allowed : 17.20 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.90 (0.35), residues: 563 helix: -3.02 (0.97), residues: 20 sheet: -0.03 (0.40), residues: 185 loop : -1.94 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 436 HIS 0.001 0.000 HIS N 66 PHE 0.017 0.001 PHE N 43 TYR 0.013 0.001 TYR H 110 ARG 0.010 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.559 Fit side-chains REVERT: L 93 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7664 (m-40) REVERT: H 74 ASP cc_start: 0.8520 (m-30) cc_final: 0.8211 (m-30) REVERT: H 114 ASP cc_start: 0.9079 (t0) cc_final: 0.8819 (t0) REVERT: R 455 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9062 (tt) outliers start: 20 outliers final: 12 residues processed: 112 average time/residue: 0.1846 time to fit residues: 25.7006 Evaluate side-chains 103 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 455 LEU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4803 Z= 0.282 Angle : 0.697 8.189 6519 Z= 0.358 Chirality : 0.047 0.225 701 Planarity : 0.005 0.092 835 Dihedral : 7.298 42.267 708 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 3.80 % Allowed : 18.60 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.87 (0.35), residues: 563 helix: -2.85 (1.00), residues: 20 sheet: 0.08 (0.37), residues: 209 loop : -2.14 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 436 HIS 0.001 0.001 HIS N 66 PHE 0.023 0.002 PHE N 43 TYR 0.014 0.001 TYR H 110 ARG 0.009 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.494 Fit side-chains REVERT: N 52 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7581 (tm-30) outliers start: 19 outliers final: 15 residues processed: 109 average time/residue: 0.1904 time to fit residues: 25.7560 Evaluate side-chains 106 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4803 Z= 0.290 Angle : 0.709 8.464 6519 Z= 0.368 Chirality : 0.046 0.181 701 Planarity : 0.006 0.092 835 Dihedral : 6.464 38.999 708 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 4.20 % Allowed : 19.20 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.89 (0.35), residues: 563 helix: -2.89 (0.98), residues: 20 sheet: 0.02 (0.37), residues: 212 loop : -2.13 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 436 HIS 0.001 0.001 HIS N 49 PHE 0.031 0.002 PHE N 43 TYR 0.017 0.001 TYR H 110 ARG 0.011 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.560 Fit side-chains REVERT: N 44 ARG cc_start: 0.5678 (ttm170) cc_final: 0.4485 (mpt180) REVERT: N 52 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7668 (pp30) outliers start: 21 outliers final: 18 residues processed: 107 average time/residue: 0.2111 time to fit residues: 27.6519 Evaluate side-chains 107 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.4980 chunk 5 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 ASN R 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 4803 Z= 0.269 Angle : 0.760 20.344 6519 Z= 0.389 Chirality : 0.047 0.298 701 Planarity : 0.005 0.081 835 Dihedral : 6.103 38.474 708 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 4.20 % Allowed : 20.80 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.78 (0.35), residues: 563 helix: -2.77 (1.03), residues: 20 sheet: 0.00 (0.37), residues: 205 loop : -1.94 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 436 HIS 0.001 0.001 HIS N 49 PHE 0.034 0.002 PHE N 43 TYR 0.016 0.001 TYR H 110 ARG 0.011 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.536 Fit side-chains REVERT: L 74 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8417 (p) REVERT: L 81 GLU cc_start: 0.6397 (tp30) cc_final: 0.6101 (tp30) REVERT: N 44 ARG cc_start: 0.6200 (ttm170) cc_final: 0.4609 (mpt180) REVERT: N 52 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7692 (pp30) outliers start: 21 outliers final: 16 residues processed: 107 average time/residue: 0.1990 time to fit residues: 26.3808 Evaluate side-chains 103 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 55 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4803 Z= 0.253 Angle : 0.747 18.623 6519 Z= 0.384 Chirality : 0.047 0.277 701 Planarity : 0.005 0.083 835 Dihedral : 5.854 37.696 708 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 4.00 % Allowed : 21.60 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.72 (0.35), residues: 563 helix: -2.70 (1.05), residues: 20 sheet: 0.23 (0.39), residues: 190 loop : -1.95 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 436 HIS 0.002 0.001 HIS N 49 PHE 0.031 0.002 PHE N 43 TYR 0.014 0.001 TYR H 110 ARG 0.013 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 1.453 Fit side-chains REVERT: L 74 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8420 (p) REVERT: L 81 GLU cc_start: 0.6388 (tp30) cc_final: 0.6102 (tp30) REVERT: N 52 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7733 (pp30) outliers start: 20 outliers final: 16 residues processed: 102 average time/residue: 0.2396 time to fit residues: 30.9637 Evaluate side-chains 105 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.0370 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4803 Z= 0.280 Angle : 0.757 16.724 6519 Z= 0.392 Chirality : 0.047 0.286 701 Planarity : 0.005 0.079 835 Dihedral : 5.785 37.353 708 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 3.80 % Allowed : 22.20 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.76 (0.35), residues: 563 helix: -3.19 (0.82), residues: 26 sheet: 0.24 (0.38), residues: 200 loop : -2.01 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 436 HIS 0.001 0.001 HIS N 49 PHE 0.031 0.002 PHE N 43 TYR 0.016 0.001 TYR H 110 ARG 0.012 0.001 ARG L 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.495 Fit side-chains REVERT: L 74 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8437 (p) REVERT: L 81 GLU cc_start: 0.6413 (tp30) cc_final: 0.6111 (tp30) REVERT: R 493 GLN cc_start: 0.8301 (mm-40) cc_final: 0.8027 (mm-40) REVERT: N 52 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7812 (pp30) outliers start: 19 outliers final: 17 residues processed: 100 average time/residue: 0.1982 time to fit residues: 24.7136 Evaluate side-chains 107 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.0270 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.142931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112674 restraints weight = 6551.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114095 restraints weight = 5980.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114642 restraints weight = 4818.213| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4803 Z= 0.243 Angle : 0.735 15.820 6519 Z= 0.379 Chirality : 0.046 0.265 701 Planarity : 0.005 0.080 835 Dihedral : 5.633 36.415 708 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 3.60 % Allowed : 22.80 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -1.71 (0.35), residues: 563 helix: -3.14 (0.85), residues: 26 sheet: 0.24 (0.39), residues: 190 loop : -1.87 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 436 HIS 0.001 0.001 HIS N 49 PHE 0.030 0.002 PHE N 43 TYR 0.014 0.001 TYR H 110 ARG 0.012 0.001 ARG L 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1515.41 seconds wall clock time: 28 minutes 31.18 seconds (1711.18 seconds total)