Starting phenix.real_space_refine on Fri Dec 27 18:45:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7phg_13415/12_2024/7phg_13415_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7phg_13415/12_2024/7phg_13415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7phg_13415/12_2024/7phg_13415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7phg_13415/12_2024/7phg_13415.map" model { file = "/net/cci-nas-00/data/ceres_data/7phg_13415/12_2024/7phg_13415_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7phg_13415/12_2024/7phg_13415_neut.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 S 18 5.16 5 C 2093 2.51 5 N 558 2.21 5 O 640 1.98 5 H 3160 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6469 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3022 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1819 Classifications: {'peptide': 123} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1628 Classifications: {'peptide': 108} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Time building chain proxies: 5.24, per 1000 atoms: 0.81 Number of scatterers: 6469 At special positions: 0 Unit cell: (72.98, 52.48, 100.04, 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 18 16.00 O 640 8.00 N 558 7.00 C 2093 6.00 H 3160 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 609.6 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 8.7% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.790A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.989A pdb=" N GLN H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.115A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.762A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 377 through 380 Processing sheet with id=AA3, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.108A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP H 50 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN H 56 " --> pdb=" O VAL H 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 93 through 94 Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.411A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.524A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) 70 hydrogen bonds defined for protein. 159 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: 2.11 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3160 1.03 - 1.23: 4 1.23 - 1.42: 1500 1.42 - 1.62: 1866 1.62 - 1.82: 22 Bond restraints: 6552 Sorted by residual: bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.76e+00 bond pdb=" CA VAL A 524 " pdb=" CB VAL A 524 " ideal model delta sigma weight residual 1.530 1.542 -0.013 1.11e-02 8.12e+03 1.30e+00 bond pdb=" C PHE H 29 " pdb=" N THR H 30 " ideal model delta sigma weight residual 1.332 1.318 0.014 1.40e-02 5.10e+03 1.07e+00 bond pdb=" CB PHE L 98 " pdb=" CG PHE L 98 " ideal model delta sigma weight residual 1.502 1.479 0.023 2.30e-02 1.89e+03 9.63e-01 bond pdb=" CA ILE H 48 " pdb=" CB ILE H 48 " ideal model delta sigma weight residual 1.545 1.532 0.013 1.45e-02 4.76e+03 8.24e-01 ... (remaining 6547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 11425 1.47 - 2.94: 273 2.94 - 4.40: 38 4.40 - 5.87: 5 5.87 - 7.34: 2 Bond angle restraints: 11743 Sorted by residual: angle pdb=" N ILE H 48 " pdb=" CA ILE H 48 " pdb=" C ILE H 48 " ideal model delta sigma weight residual 111.62 104.28 7.34 7.90e-01 1.60e+00 8.63e+01 angle pdb=" N TRP H 47 " pdb=" CA TRP H 47 " pdb=" C TRP H 47 " ideal model delta sigma weight residual 110.24 116.38 -6.14 1.30e+00 5.92e-01 2.23e+01 angle pdb=" N GLY A 381 " pdb=" CA GLY A 381 " pdb=" C GLY A 381 " ideal model delta sigma weight residual 113.58 109.75 3.83 1.07e+00 8.73e-01 1.28e+01 angle pdb=" C TRP H 47 " pdb=" CA TRP H 47 " pdb=" CB TRP H 47 " ideal model delta sigma weight residual 109.64 104.40 5.24 1.77e+00 3.19e-01 8.76e+00 angle pdb=" C PRO A 463 " pdb=" N PHE A 464 " pdb=" CA PHE A 464 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.79e+00 ... (remaining 11738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 2777 16.08 - 32.15: 262 32.15 - 48.22: 80 48.22 - 64.30: 37 64.30 - 80.37: 8 Dihedral angle restraints: 3164 sinusoidal: 1677 harmonic: 1487 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 28.65 64.35 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -143.11 57.11 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CB CYS H 97 " pdb=" SG CYS H 97 " pdb=" SG CYS H 100B" pdb=" CB CYS H 100B" ideal model delta sinusoidal sigma weight residual -86.00 -45.36 -40.64 1 1.00e+01 1.00e-02 2.32e+01 ... (remaining 3161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 349 0.042 - 0.083: 101 0.083 - 0.125: 36 0.125 - 0.167: 5 0.167 - 0.209: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE H 48 " pdb=" N ILE H 48 " pdb=" C ILE H 48 " pdb=" CB ILE H 48 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA TRP H 47 " pdb=" N TRP H 47 " pdb=" C TRP H 47 " pdb=" CB TRP H 47 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA PRO L 80 " pdb=" N PRO L 80 " pdb=" C PRO L 80 " pdb=" CB PRO L 80 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 489 not shown) Planarity restraints: 1002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " 0.022 2.00e-02 2.50e+03 1.06e-02 4.46e+00 pdb=" CG TRP H 47 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP H 47 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP H 47 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 47 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 47 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP H 47 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 94 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO L 95 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 35 " 0.009 2.00e-02 2.50e+03 7.85e-03 2.46e+00 pdb=" CG TRP L 35 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP L 35 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP L 35 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 35 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP L 35 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 35 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 35 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 35 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 35 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP L 35 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP L 35 " 0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP L 35 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP L 35 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP L 35 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP L 35 " 0.002 2.00e-02 2.50e+03 ... (remaining 999 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 210 2.10 - 2.72: 11442 2.72 - 3.35: 18874 3.35 - 3.97: 24223 3.97 - 4.60: 37018 Nonbonded interactions: 91767 Sorted by model distance: nonbonded pdb=" H TYR A 453 " pdb=" O GLN A 493 " model vdw 1.473 2.450 nonbonded pdb="HH22 ARG H 66 " pdb=" OD2 ASP H 86 " model vdw 1.594 2.450 nonbonded pdb=" H GLN A 498 " pdb=" OD1 ASN A 501 " model vdw 1.604 2.450 nonbonded pdb=" OE1 GLN H 6 " pdb=" H GLY H 106 " model vdw 1.608 2.450 nonbonded pdb=" O SER L 76 " pdb=" HE ARG L 77 " model vdw 1.641 2.450 ... (remaining 91762 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: 7.430 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: 0.130 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 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 : 0.003 0.041 3392 Z= 0.208 Angle : 0.677 7.339 4608 Z= 0.402 Chirality : 0.045 0.209 492 Planarity : 0.005 0.046 599 Dihedral : 13.712 80.375 1206 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.37), residues: 421 helix: -4.42 (0.50), residues: 19 sheet: -2.65 (0.38), residues: 124 loop : -2.28 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP H 47 HIS 0.000 0.000 HIS A 519 PHE 0.017 0.002 PHE A 347 TYR 0.027 0.002 TYR L 87 ARG 0.004 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7500 (tmm160) cc_final: 0.7146 (tmt170) REVERT: A 351 TYR cc_start: 0.7985 (p90) cc_final: 0.7743 (p90) REVERT: A 394 ASN cc_start: 0.8238 (m110) cc_final: 0.7884 (m110) REVERT: A 512 VAL cc_start: 0.8767 (t) cc_final: 0.8529 (t) REVERT: H 2 MET cc_start: 0.5821 (mmp) cc_final: 0.5591 (mmp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.4023 time to fit residues: 40.2269 Evaluate side-chains 70 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.0870 chunk 20 optimal weight: 0.2980 chunk 16 optimal weight: 0.0970 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 3392 Z= 0.217 Angle : 0.657 16.882 4608 Z= 0.348 Chirality : 0.046 0.236 492 Planarity : 0.005 0.039 599 Dihedral : 5.817 28.843 471 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.35 % Favored : 87.65 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.38), residues: 421 helix: -4.10 (0.58), residues: 19 sheet: -2.55 (0.40), residues: 119 loop : -2.36 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 HIS 0.000 0.000 HIS A 519 PHE 0.012 0.002 PHE A 347 TYR 0.012 0.001 TYR L 91 ARG 0.003 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.8221 (m110) cc_final: 0.7885 (m110) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.4005 time to fit residues: 39.1736 Evaluate side-chains 74 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 0.0870 chunk 40 optimal weight: 0.4980 chunk 33 optimal weight: 0.2980 chunk 36 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 3392 Z= 0.262 Angle : 0.640 14.224 4608 Z= 0.343 Chirality : 0.044 0.214 492 Planarity : 0.005 0.044 599 Dihedral : 5.763 28.962 471 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.37), residues: 421 helix: -3.55 (0.69), residues: 27 sheet: -2.64 (0.40), residues: 119 loop : -2.45 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.011 0.002 PHE A 392 TYR 0.012 0.002 TYR L 87 ARG 0.003 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7582 (tmm160) cc_final: 0.6815 (ptm-80) REVERT: A 394 ASN cc_start: 0.8289 (m110) cc_final: 0.7979 (m110) REVERT: A 427 ASP cc_start: 0.7680 (m-30) cc_final: 0.7478 (m-30) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.4466 time to fit residues: 44.2785 Evaluate side-chains 73 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 17 optimal weight: 0.0370 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.0870 chunk 39 optimal weight: 0.0980 chunk 35 optimal weight: 0.0970 chunk 10 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 overall best weight: 0.1234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 3392 Z= 0.190 Angle : 0.609 12.405 4608 Z= 0.323 Chirality : 0.045 0.186 492 Planarity : 0.005 0.043 599 Dihedral : 5.612 26.808 471 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.39), residues: 421 helix: -3.41 (0.74), residues: 27 sheet: -2.53 (0.44), residues: 110 loop : -2.27 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 HIS 0.000 0.000 HIS A 519 PHE 0.008 0.001 PHE A 400 TYR 0.012 0.001 TYR A 369 ARG 0.005 0.000 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7664 (tmm160) cc_final: 0.7026 (ptm-80) REVERT: A 394 ASN cc_start: 0.8330 (m110) cc_final: 0.8087 (m110) REVERT: A 427 ASP cc_start: 0.7680 (m-30) cc_final: 0.7435 (m-30) REVERT: A 453 TYR cc_start: 0.6891 (m-80) cc_final: 0.6687 (m-10) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.4102 time to fit residues: 45.0689 Evaluate side-chains 78 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.0270 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 10 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 overall best weight: 0.3038 ------------------------------------------------------------------------------- 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: 0.6891 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 3392 Z= 0.254 Angle : 0.609 11.535 4608 Z= 0.326 Chirality : 0.044 0.175 492 Planarity : 0.004 0.043 599 Dihedral : 5.675 28.743 471 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.78 % Favored : 86.22 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.39), residues: 421 helix: -3.23 (0.79), residues: 27 sheet: -2.71 (0.43), residues: 110 loop : -2.21 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 47 HIS 0.001 0.001 HIS A 519 PHE 0.010 0.001 PHE A 392 TYR 0.012 0.001 TYR A 489 ARG 0.002 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7687 (tmm160) cc_final: 0.7133 (ptm-80) REVERT: A 394 ASN cc_start: 0.8314 (m110) cc_final: 0.8062 (m-40) REVERT: A 427 ASP cc_start: 0.7666 (m-30) cc_final: 0.7433 (m-30) REVERT: A 451 TYR cc_start: 0.7538 (m-10) cc_final: 0.7285 (m-10) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.3869 time to fit residues: 41.4662 Evaluate side-chains 80 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 3 optimal weight: 0.0970 chunk 13 optimal weight: 0.0980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 overall best weight: 0.2556 ------------------------------------------------------------------------------- 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: 0.6892 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3392 Z= 0.229 Angle : 0.614 11.230 4608 Z= 0.327 Chirality : 0.044 0.147 492 Planarity : 0.004 0.044 599 Dihedral : 5.709 28.461 471 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.39), residues: 421 helix: -3.18 (0.81), residues: 27 sheet: -2.71 (0.44), residues: 110 loop : -2.20 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 HIS 0.000 0.000 HIS A 519 PHE 0.009 0.001 PHE A 400 TYR 0.015 0.002 TYR A 380 ARG 0.004 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7667 (tmm160) cc_final: 0.7122 (ptm-80) REVERT: A 351 TYR cc_start: 0.8095 (p90) cc_final: 0.7808 (p90) REVERT: A 394 ASN cc_start: 0.8336 (m110) cc_final: 0.8095 (m-40) REVERT: A 427 ASP cc_start: 0.7725 (m-30) cc_final: 0.7513 (m-30) REVERT: A 451 TYR cc_start: 0.7551 (m-10) cc_final: 0.7330 (m-10) REVERT: A 513 LEU cc_start: 0.8886 (tt) cc_final: 0.8678 (tt) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.4509 time to fit residues: 48.7055 Evaluate side-chains 79 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.3980 chunk 22 optimal weight: 0.3980 chunk 33 optimal weight: 0.0980 chunk 39 optimal weight: 0.1980 chunk 24 optimal weight: 0.0980 chunk 18 optimal weight: 0.0470 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 25 optimal weight: 0.0570 overall best weight: 0.0774 ------------------------------------------------------------------------------- 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: 0.6808 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 3392 Z= 0.191 Angle : 0.608 10.646 4608 Z= 0.325 Chirality : 0.045 0.150 492 Planarity : 0.004 0.043 599 Dihedral : 5.602 28.179 471 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.39), residues: 421 helix: -3.04 (0.86), residues: 27 sheet: -2.49 (0.45), residues: 115 loop : -2.21 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP L 35 HIS 0.000 0.000 HIS A 519 PHE 0.012 0.001 PHE A 392 TYR 0.015 0.002 TYR A 380 ARG 0.005 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7684 (tmm160) cc_final: 0.7124 (ptm-80) REVERT: A 394 ASN cc_start: 0.8326 (m110) cc_final: 0.8092 (m-40) REVERT: A 427 ASP cc_start: 0.7721 (m-30) cc_final: 0.7501 (m-30) REVERT: A 451 TYR cc_start: 0.7448 (m-10) cc_final: 0.7239 (m-10) REVERT: A 513 LEU cc_start: 0.8855 (tt) cc_final: 0.8653 (tt) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.3682 time to fit residues: 39.3552 Evaluate side-chains 77 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.0870 chunk 35 optimal weight: 0.0980 chunk 37 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 chunk 22 optimal weight: 0.0770 chunk 16 optimal weight: 0.0870 chunk 28 optimal weight: 0.1980 overall best weight: 0.0892 ------------------------------------------------------------------------------- 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: 0.6778 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 3392 Z= 0.177 Angle : 0.589 9.888 4608 Z= 0.316 Chirality : 0.044 0.143 492 Planarity : 0.005 0.044 599 Dihedral : 5.522 27.986 471 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.40), residues: 421 helix: -2.91 (0.92), residues: 27 sheet: -2.67 (0.44), residues: 110 loop : -2.10 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 47 HIS 0.000 0.000 HIS A 519 PHE 0.009 0.001 PHE A 374 TYR 0.013 0.002 TYR A 453 ARG 0.007 0.001 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7675 (tmm160) cc_final: 0.7098 (ptm-80) REVERT: A 394 ASN cc_start: 0.8354 (m110) cc_final: 0.8140 (m-40) REVERT: A 427 ASP cc_start: 0.7738 (m-30) cc_final: 0.7510 (m-30) REVERT: A 513 LEU cc_start: 0.8868 (tt) cc_final: 0.8664 (tt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.3955 time to fit residues: 41.1329 Evaluate side-chains 74 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 36 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 37 optimal weight: 0.0980 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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: 0.6874 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3392 Z= 0.243 Angle : 0.624 10.744 4608 Z= 0.335 Chirality : 0.044 0.144 492 Planarity : 0.004 0.043 599 Dihedral : 5.664 28.201 471 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.25 % Favored : 85.75 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.39), residues: 421 helix: -2.95 (0.89), residues: 27 sheet: -2.55 (0.47), residues: 104 loop : -2.17 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 35 HIS 0.001 0.000 HIS A 519 PHE 0.013 0.001 PHE A 392 TYR 0.013 0.002 TYR A 380 ARG 0.003 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7651 (tmm160) cc_final: 0.7103 (ptm-80) REVERT: A 427 ASP cc_start: 0.7762 (m-30) cc_final: 0.7511 (m-30) REVERT: A 512 VAL cc_start: 0.8915 (t) cc_final: 0.8563 (p) REVERT: A 513 LEU cc_start: 0.8872 (tt) cc_final: 0.8662 (tt) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.4166 time to fit residues: 43.5243 Evaluate side-chains 77 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 0.0770 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 29 optimal weight: 0.0870 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 33 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 overall best weight: 0.1914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 3392 Z= 0.201 Angle : 0.616 10.403 4608 Z= 0.327 Chirality : 0.044 0.143 492 Planarity : 0.004 0.044 599 Dihedral : 5.627 28.760 471 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.35 % Favored : 87.65 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.39), residues: 421 helix: -3.17 (0.85), residues: 27 sheet: -2.59 (0.46), residues: 105 loop : -2.16 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 47 HIS 0.000 0.000 HIS A 519 PHE 0.008 0.001 PHE A 400 TYR 0.023 0.002 TYR A 473 ARG 0.004 0.000 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7648 (tmm160) cc_final: 0.7108 (ptm-80) REVERT: A 427 ASP cc_start: 0.7716 (m-30) cc_final: 0.7465 (m-30) REVERT: A 513 LEU cc_start: 0.8904 (tt) cc_final: 0.8698 (tt) REVERT: H 2 MET cc_start: 0.6408 (mmp) cc_final: 0.6188 (mmp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.4178 time to fit residues: 43.4289 Evaluate side-chains 78 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 23 optimal weight: 0.2980 chunk 37 optimal weight: 0.0370 chunk 21 optimal weight: 0.2980 chunk 27 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 16 optimal weight: 0.0980 chunk 15 optimal weight: 0.0980 chunk 40 optimal weight: 0.0870 overall best weight: 0.0834 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.111472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.105246 restraints weight = 21775.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.107657 restraints weight = 10827.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.109072 restraints weight = 5900.585| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 3392 Z= 0.175 Angle : 0.593 9.374 4608 Z= 0.315 Chirality : 0.044 0.141 492 Planarity : 0.004 0.044 599 Dihedral : 5.472 27.829 471 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.40), residues: 421 helix: -2.94 (0.92), residues: 27 sheet: -2.64 (0.45), residues: 110 loop : -2.09 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 47 HIS 0.000 0.000 HIS A 519 PHE 0.010 0.001 PHE A 400 TYR 0.022 0.002 TYR A 473 ARG 0.004 0.000 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4146.47 seconds wall clock time: 74 minutes 39.62 seconds (4479.62 seconds total)