Starting phenix.real_space_refine on Mon Mar 11 01:35:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phg_13415/03_2024/7phg_13415_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phg_13415/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phg_13415/03_2024/7phg_13415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phg_13415/03_2024/7phg_13415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phg_13415/03_2024/7phg_13415_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phg_13415/03_2024/7phg_13415_neut.pdb" } 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 Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.47, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.60 Conformation dependent library (CDL) restraints added in 703.5 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: 0.53 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: 2.21 Time building geometry restraints manager: 5.63 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: 100.07 - 106.84: 132 106.84 - 113.62: 7381 113.62 - 120.40: 2216 120.40 - 127.17: 1975 127.17 - 133.95: 39 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 1.850 nonbonded pdb="HH22 ARG H 66 " pdb=" OD2 ASP H 86 " model vdw 1.594 1.850 nonbonded pdb=" H GLN A 498 " pdb=" OD1 ASN A 501 " model vdw 1.604 1.850 nonbonded pdb=" OE1 GLN H 6 " pdb=" H GLY H 106 " model vdw 1.608 1.850 nonbonded pdb=" O SER L 76 " pdb=" HE ARG L 77 " model vdw 1.641 1.850 ... (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 ========== 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: 9.600 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: 0.110 Extract box with map and model: 27.530 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 25.800 Find NCS groups from input model: 0.110 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.130 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.548 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: 0.3914 time to fit residues: 39.1919 Evaluate side-chains 70 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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: 0.3980 chunk 31 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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: 0.6948 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 3392 Z= 0.288 Angle : 0.665 17.273 4608 Z= 0.352 Chirality : 0.045 0.254 492 Planarity : 0.005 0.040 599 Dihedral : 5.851 29.241 471 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.78 % Favored : 86.22 % Rotamer: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % 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: -3.91 (0.37), residues: 421 helix: -3.68 (0.65), residues: 27 sheet: -2.73 (0.39), residues: 119 loop : -2.52 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.001 0.001 HIS A 519 PHE 0.013 0.002 PHE A 342 TYR 0.012 0.002 TYR H 90 ARG 0.002 0.001 ARG A 454 *********************** 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 fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.481 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: A 394 ASN cc_start: 0.8286 (m110) cc_final: 0.7978 (m110) REVERT: H 2 MET cc_start: 0.6075 (mmp) cc_final: 0.5759 (mmp) REVERT: L 104 VAL cc_start: 0.8434 (t) cc_final: 0.8124 (m) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3823 time to fit residues: 37.2861 Evaluate side-chains 72 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 chunk 37 optimal weight: 0.2980 chunk 40 optimal weight: 0.0770 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 overall best weight: 0.2516 ------------------------------------------------------------------------------- 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: 0.6913 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 3392 Z= 0.242 Angle : 0.632 14.393 4608 Z= 0.336 Chirality : 0.044 0.215 492 Planarity : 0.005 0.044 599 Dihedral : 5.743 29.857 471 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: -3.85 (0.37), residues: 421 helix: -3.78 (0.63), residues: 27 sheet: -2.74 (0.39), residues: 119 loop : -2.44 (0.37), residues: 275 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 0.010 0.002 PHE A 392 TYR 0.011 0.001 TYR L 87 ARG 0.003 0.001 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 85 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.400 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: 0.7624 (tmm160) cc_final: 0.6886 (ptm-80) REVERT: A 394 ASN cc_start: 0.8357 (m110) cc_final: 0.8079 (m110) REVERT: A 427 ASP cc_start: 0.7671 (m-30) cc_final: 0.7459 (m-30) REVERT: H 2 MET cc_start: 0.6286 (mmp) cc_final: 0.5874 (mmp) REVERT: H 36 TRP cc_start: 0.8186 (m100) cc_final: 0.7679 (m100) REVERT: L 104 VAL cc_start: 0.8458 (t) cc_final: 0.8100 (m) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3882 time to fit residues: 38.8963 Evaluate side-chains 76 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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: 0.5980 chunk 19 optimal weight: 0.0970 chunk 4 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 37 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 0.0970 chunk 10 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 overall best weight: 0.2176 ------------------------------------------------------------------------------- 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: 0.6906 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 3392 Z= 0.217 Angle : 0.605 12.393 4608 Z= 0.321 Chirality : 0.044 0.191 492 Planarity : 0.004 0.043 599 Dihedral : 5.614 28.408 471 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: -3.81 (0.38), residues: 421 helix: -3.78 (0.62), residues: 27 sheet: -2.71 (0.40), residues: 119 loop : -2.40 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.000 0.000 HIS A 519 PHE 0.010 0.001 PHE A 400 TYR 0.011 0.001 TYR A 369 ARG 0.005 0.001 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 87 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.519 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 346 ARG cc_start: 0.7785 (tmm160) cc_final: 0.7187 (ptm-80) REVERT: A 394 ASN cc_start: 0.8366 (m110) cc_final: 0.8114 (m-40) REVERT: A 427 ASP cc_start: 0.7715 (m-30) cc_final: 0.7482 (m-30) REVERT: H 2 MET cc_start: 0.6389 (mmp) cc_final: 0.6071 (mmp) REVERT: H 36 TRP cc_start: 0.8241 (m100) cc_final: 0.7740 (m100) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.3993 time to fit residues: 40.7135 Evaluate side-chains 74 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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: 0.9980 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 7 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.7038 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 3392 Z= 0.364 Angle : 0.657 11.661 4608 Z= 0.356 Chirality : 0.044 0.181 492 Planarity : 0.005 0.044 599 Dihedral : 5.960 29.939 471 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.44 % Favored : 84.56 % Rotamer: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % 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: -3.95 (0.37), residues: 421 helix: -3.94 (0.58), residues: 27 sheet: -2.91 (0.40), residues: 119 loop : -2.43 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 47 HIS 0.002 0.001 HIS A 519 PHE 0.015 0.002 PHE A 400 TYR 0.010 0.002 TYR A 351 ARG 0.003 0.001 ARG A 454 *********************** 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 fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.538 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: 0.7846 (tmm160) cc_final: 0.7348 (ptm-80) REVERT: A 351 TYR cc_start: 0.8301 (p90) cc_final: 0.8010 (p90) REVERT: A 394 ASN cc_start: 0.8337 (m110) cc_final: 0.8110 (m-40) REVERT: A 427 ASP cc_start: 0.7675 (m-30) cc_final: 0.7440 (m-30) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.3940 time to fit residues: 42.1200 Evaluate side-chains 81 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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: 0.8980 chunk 39 optimal weight: 0.0980 chunk 32 optimal weight: 0.0970 chunk 18 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 overall best weight: 0.0974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 3392 Z= 0.186 Angle : 0.604 11.482 4608 Z= 0.322 Chirality : 0.045 0.155 492 Planarity : 0.004 0.043 599 Dihedral : 5.718 32.072 471 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.81 (0.38), residues: 421 helix: -3.91 (0.60), residues: 27 sheet: -2.88 (0.41), residues: 110 loop : -2.34 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP L 35 HIS 0.000 0.000 HIS A 519 PHE 0.010 0.001 PHE A 400 TYR 0.012 0.002 TYR A 369 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 89 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.834 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: 0.7740 (tmm160) cc_final: 0.7200 (ptm-80) REVERT: A 394 ASN cc_start: 0.8362 (m110) cc_final: 0.8144 (m-40) REVERT: A 427 ASP cc_start: 0.7695 (m-30) cc_final: 0.7468 (m-30) REVERT: H 2 MET cc_start: 0.6498 (mmp) cc_final: 0.6203 (mmp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.3824 time to fit residues: 40.2247 Evaluate side-chains 77 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 0.0980 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 0.1980 chunk 24 optimal weight: 0.2980 chunk 18 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 overall best weight: 0.2380 ------------------------------------------------------------------------------- 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: 0.6913 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 3392 Z= 0.239 Angle : 0.609 10.925 4608 Z= 0.327 Chirality : 0.044 0.160 492 Planarity : 0.004 0.043 599 Dihedral : 5.751 32.819 471 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.44 % Favored : 84.56 % 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 : 0.25 % 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: -3.79 (0.38), residues: 421 helix: -3.91 (0.61), residues: 27 sheet: -2.89 (0.42), residues: 110 loop : -2.32 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 47 HIS 0.001 0.000 HIS A 519 PHE 0.010 0.001 PHE A 400 TYR 0.017 0.002 TYR A 380 ARG 0.004 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 90 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.525 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: 0.7817 (tmm160) cc_final: 0.7275 (ptm-80) REVERT: A 394 ASN cc_start: 0.8325 (m110) cc_final: 0.8109 (m-40) REVERT: A 427 ASP cc_start: 0.7683 (m-30) cc_final: 0.7446 (m-30) REVERT: H 2 MET cc_start: 0.6607 (mmp) cc_final: 0.6364 (mmm) REVERT: H 39 GLN cc_start: 0.6906 (tp40) cc_final: 0.6522 (tp40) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.3795 time to fit residues: 40.5642 Evaluate side-chains 78 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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: 0.2980 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 35 optimal weight: 0.4980 chunk 37 optimal weight: 0.0870 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.0040 chunk 28 optimal weight: 0.2980 overall best weight: 0.2370 ------------------------------------------------------------------------------- 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: 0.6909 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 3392 Z= 0.224 Angle : 0.597 10.389 4608 Z= 0.320 Chirality : 0.044 0.152 492 Planarity : 0.004 0.043 599 Dihedral : 5.725 33.300 471 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.30 % Favored : 86.70 % 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 : 0.25 % 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: -3.73 (0.38), residues: 421 helix: -3.81 (0.65), residues: 27 sheet: -2.71 (0.44), residues: 109 loop : -2.34 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 47 HIS 0.000 0.000 HIS A 519 PHE 0.012 0.001 PHE A 400 TYR 0.015 0.002 TYR A 380 ARG 0.005 0.001 ARG L 18 *********************** 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 92 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.631 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: 0.7799 (tmm160) cc_final: 0.7311 (ptm-80) REVERT: A 427 ASP cc_start: 0.7690 (m-30) cc_final: 0.7421 (m-30) REVERT: H 2 MET cc_start: 0.6730 (mmp) cc_final: 0.6360 (mmp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.4234 time to fit residues: 45.3767 Evaluate side-chains 80 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 37 optimal weight: 0.0970 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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: 0.6945 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3392 Z= 0.267 Angle : 0.619 11.176 4608 Z= 0.333 Chirality : 0.044 0.142 492 Planarity : 0.005 0.043 599 Dihedral : 5.801 33.389 471 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.20 % Favored : 84.80 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.77 (0.38), residues: 421 helix: -3.73 (0.68), residues: 27 sheet: -2.83 (0.44), residues: 104 loop : -2.37 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 47 HIS 0.001 0.001 HIS A 519 PHE 0.014 0.002 PHE A 400 TYR 0.015 0.002 TYR A 380 ARG 0.004 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 89 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.471 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: 0.7849 (tmm160) cc_final: 0.7357 (ptm-80) REVERT: A 427 ASP cc_start: 0.7704 (m-30) cc_final: 0.7438 (m-30) REVERT: H 2 MET cc_start: 0.6781 (mmp) cc_final: 0.6295 (mmp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.3942 time to fit residues: 41.0225 Evaluate side-chains 80 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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: 0.9980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 13 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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: 0.6997 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 3392 Z= 0.308 Angle : 0.661 11.422 4608 Z= 0.356 Chirality : 0.045 0.153 492 Planarity : 0.005 0.043 599 Dihedral : 5.999 33.206 471 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 22.41 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 : 0.25 % 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: -3.89 (0.38), residues: 421 helix: -3.71 (0.69), residues: 27 sheet: -2.95 (0.42), residues: 109 loop : -2.42 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.004 TRP L 35 HIS 0.001 0.001 HIS A 519 PHE 0.015 0.002 PHE A 400 TYR 0.020 0.002 TYR H 59 ARG 0.005 0.001 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 89 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.531 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: 0.7894 (tmm160) cc_final: 0.7404 (ptm160) REVERT: A 427 ASP cc_start: 0.7719 (m-30) cc_final: 0.7459 (m-30) REVERT: H 2 MET cc_start: 0.6803 (mmp) cc_final: 0.6501 (mmp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.4061 time to fit residues: 42.3855 Evaluate side-chains 80 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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: 0.8980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 26 optimal weight: 0.2980 chunk 24 optimal weight: 0.1980 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 overall best weight: 0.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.107028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.100800 restraints weight = 21898.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.103219 restraints weight = 10429.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.104577 restraints weight = 5542.461| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3392 Z= 0.234 Angle : 0.627 10.985 4608 Z= 0.335 Chirality : 0.044 0.149 492 Planarity : 0.005 0.044 599 Dihedral : 5.864 33.420 471 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.06 % Favored : 86.94 % 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 : 0.25 % 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 (0.38), residues: 421 helix: -3.68 (0.71), residues: 27 sheet: -2.89 (0.43), residues: 104 loop : -2.39 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRP L 35 HIS 0.000 0.000 HIS A 519 PHE 0.011 0.001 PHE A 400 TYR 0.012 0.002 TYR A 369 ARG 0.005 0.001 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3844.99 seconds wall clock time: 68 minutes 40.44 seconds (4120.44 seconds total)