Starting phenix.real_space_refine on Mon Sep 23 14:24:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdo_13922/09_2024/7qdo_13922.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdo_13922/09_2024/7qdo_13922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdo_13922/09_2024/7qdo_13922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdo_13922/09_2024/7qdo_13922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdo_13922/09_2024/7qdo_13922.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdo_13922/09_2024/7qdo_13922.cif" } resolution = 3.6 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= 0.004 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2080 2.51 5 N 564 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3304 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1652 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 194} Restraints were copied for chains: B Time building chain proxies: 3.06, per 1000 atoms: 0.93 Number of scatterers: 3304 At special positions: 0 Unit cell: (84.739, 52.857, 80.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 648 8.00 N 564 7.00 C 2080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.04 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 404.6 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 816 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 12 sheets defined 11.3% alpha, 38.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 414 through 421 removed outlier: 4.006A pdb=" N TRP B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 530 Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 414 through 421 removed outlier: 4.006A pdb=" N TRP A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 Processing sheet with id=AA1, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.641A pdb=" N ARG B 346 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 366 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 363 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 411 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS B 367 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 409 " --> pdb=" O CYS B 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 380 through 383 removed outlier: 3.704A pdb=" N VAL B 428 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 399 through 400 removed outlier: 3.966A pdb=" N THR B 404 " --> pdb=" O HIS B 400 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 453 through 457 removed outlier: 6.202A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 453 through 457 removed outlier: 6.202A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 493 through 494 removed outlier: 3.595A pdb=" N CYS B 536 " --> pdb=" O ARG B 550 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 346 through 350 removed outlier: 3.641A pdb=" N ARG A 346 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 366 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR A 363 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 411 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS A 367 " --> pdb=" O GLY A 409 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A 409 " --> pdb=" O CYS A 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 380 through 383 removed outlier: 3.705A pdb=" N VAL A 428 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 399 through 400 removed outlier: 3.966A pdb=" N THR A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 453 through 457 removed outlier: 6.202A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 453 through 457 removed outlier: 6.202A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.595A pdb=" N CYS A 536 " --> pdb=" O ARG A 550 " (cutoff:3.500A) 136 hydrogen bonds defined for protein. 348 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: 0.83 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1072 1.34 - 1.46: 706 1.46 - 1.58: 1596 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3390 Sorted by residual: bond pdb=" N VAL B 447 " pdb=" CA VAL B 447 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.27e-02 6.20e+03 7.10e+00 bond pdb=" N THR A 533 " pdb=" CA THR A 533 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.23e-02 6.61e+03 6.89e+00 bond pdb=" N THR B 533 " pdb=" CA THR B 533 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.23e-02 6.61e+03 6.79e+00 bond pdb=" N VAL A 447 " pdb=" CA VAL A 447 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.27e-02 6.20e+03 6.76e+00 bond pdb=" N SER A 442 " pdb=" CA SER A 442 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.64e+00 ... (remaining 3385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 4228 1.29 - 2.58: 321 2.58 - 3.86: 75 3.86 - 5.15: 8 5.15 - 6.44: 12 Bond angle restraints: 4644 Sorted by residual: angle pdb=" N ASN A 465 " pdb=" CA ASN A 465 " pdb=" C ASN A 465 " ideal model delta sigma weight residual 114.56 108.69 5.87 1.27e+00 6.20e-01 2.14e+01 angle pdb=" N ASN B 465 " pdb=" CA ASN B 465 " pdb=" C ASN B 465 " ideal model delta sigma weight residual 114.56 108.69 5.87 1.27e+00 6.20e-01 2.14e+01 angle pdb=" N LYS A 445 " pdb=" CA LYS A 445 " pdb=" C LYS A 445 " ideal model delta sigma weight residual 114.56 110.31 4.25 1.27e+00 6.20e-01 1.12e+01 angle pdb=" CA ARG B 491 " pdb=" C ARG B 491 " pdb=" O ARG B 491 " ideal model delta sigma weight residual 122.03 118.12 3.91 1.17e+00 7.31e-01 1.11e+01 angle pdb=" N LYS B 445 " pdb=" CA LYS B 445 " pdb=" C LYS B 445 " ideal model delta sigma weight residual 114.56 110.33 4.23 1.27e+00 6.20e-01 1.11e+01 ... (remaining 4639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 1872 15.93 - 31.87: 142 31.87 - 47.80: 34 47.80 - 63.73: 0 63.73 - 79.66: 2 Dihedral angle restraints: 2050 sinusoidal: 802 harmonic: 1248 Sorted by residual: dihedral pdb=" CB CYS B 367 " pdb=" SG CYS B 367 " pdb=" SG CYS B 426 " pdb=" CB CYS B 426 " ideal model delta sinusoidal sigma weight residual 93.00 137.25 -44.25 1 1.00e+01 1.00e-02 2.72e+01 dihedral pdb=" CB CYS B 474 " pdb=" SG CYS B 474 " pdb=" SG CYS B 536 " pdb=" CB CYS B 536 " ideal model delta sinusoidal sigma weight residual 93.00 65.87 27.13 1 1.00e+01 1.00e-02 1.06e+01 dihedral pdb=" CA MET B 506 " pdb=" C MET B 506 " pdb=" N PRO B 507 " pdb=" CA PRO B 507 " ideal model delta harmonic sigma weight residual -180.00 -163.98 -16.02 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 344 0.037 - 0.074: 119 0.074 - 0.112: 65 0.112 - 0.149: 14 0.149 - 0.186: 2 Chirality restraints: 544 Sorted by residual: chirality pdb=" CA VAL B 447 " pdb=" N VAL B 447 " pdb=" C VAL B 447 " pdb=" CB VAL B 447 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" CA VAL A 447 " pdb=" N VAL A 447 " pdb=" C VAL A 447 " pdb=" CB VAL A 447 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CA LEU A 449 " pdb=" N LEU A 449 " pdb=" C LEU A 449 " pdb=" CB LEU A 449 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 541 not shown) Planarity restraints: 598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 451 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 452 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 451 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.49e+00 pdb=" N PRO B 452 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 452 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 452 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 382 " 0.007 2.00e-02 2.50e+03 7.53e-03 1.42e+00 pdb=" CG TRP A 382 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP A 382 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 382 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 382 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 382 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 382 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 382 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 382 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 382 " 0.000 2.00e-02 2.50e+03 ... (remaining 595 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 28 2.61 - 3.18: 2840 3.18 - 3.76: 4774 3.76 - 4.33: 6386 4.33 - 4.90: 10535 Nonbonded interactions: 24563 Sorted by model distance: nonbonded pdb=" SG CYS A 367 " pdb=" SG CYS A 426 " model vdw 2.038 3.760 nonbonded pdb=" SG CYS A 474 " pdb=" SG CYS A 536 " model vdw 2.041 3.760 nonbonded pdb=" OD1 ASP A 553 " pdb=" OG1 THR A 556 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASP B 553 " pdb=" OG1 THR B 556 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR B 363 " pdb=" O ILE B 413 " model vdw 2.270 3.040 ... (remaining 24558 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.960 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3390 Z= 0.337 Angle : 0.823 6.438 4644 Z= 0.510 Chirality : 0.049 0.186 544 Planarity : 0.005 0.031 598 Dihedral : 11.618 79.664 1228 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.40), residues: 420 helix: -0.82 (0.83), residues: 44 sheet: 1.32 (0.37), residues: 180 loop : -2.45 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 382 HIS 0.004 0.001 HIS A 540 PHE 0.013 0.003 PHE A 479 TYR 0.011 0.002 TYR A 500 ARG 0.004 0.001 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1720 time to fit residues: 19.7843 Evaluate side-chains 67 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3390 Z= 0.220 Angle : 0.675 6.228 4644 Z= 0.358 Chirality : 0.047 0.161 544 Planarity : 0.005 0.036 598 Dihedral : 4.230 16.473 454 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 1.85 % Allowed : 10.58 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.41), residues: 420 helix: -0.36 (0.74), residues: 44 sheet: 1.34 (0.40), residues: 174 loop : -1.77 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 488 HIS 0.007 0.001 HIS A 518 PHE 0.017 0.002 PHE A 479 TYR 0.005 0.001 TYR A 534 ARG 0.004 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 417 ASP cc_start: 0.8204 (p0) cc_final: 0.7903 (p0) REVERT: B 506 MET cc_start: 0.6590 (mmm) cc_final: 0.6098 (ptt) REVERT: A 367 CYS cc_start: 0.7497 (p) cc_final: 0.7133 (p) REVERT: A 417 ASP cc_start: 0.8152 (p0) cc_final: 0.7946 (p0) REVERT: A 506 MET cc_start: 0.6644 (mmm) cc_final: 0.6097 (ptt) outliers start: 7 outliers final: 6 residues processed: 84 average time/residue: 0.1627 time to fit residues: 16.3745 Evaluate side-chains 62 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 545 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.0050 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3390 Z= 0.187 Angle : 0.628 5.952 4644 Z= 0.328 Chirality : 0.044 0.153 544 Planarity : 0.004 0.031 598 Dihedral : 4.145 15.358 454 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.17 % Allowed : 14.29 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.40), residues: 420 helix: -0.41 (0.75), residues: 44 sheet: 1.38 (0.39), residues: 160 loop : -1.80 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 528 HIS 0.005 0.001 HIS B 518 PHE 0.013 0.002 PHE B 479 TYR 0.016 0.002 TYR A 500 ARG 0.003 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: B 438 LYS cc_start: 0.8724 (mttt) cc_final: 0.8267 (mmtt) REVERT: B 506 MET cc_start: 0.6699 (mmm) cc_final: 0.5858 (ptp) REVERT: A 367 CYS cc_start: 0.7565 (p) cc_final: 0.7117 (p) REVERT: A 489 MET cc_start: 0.7914 (tpp) cc_final: 0.7289 (mmm) REVERT: A 506 MET cc_start: 0.6641 (mmm) cc_final: 0.6073 (ptt) outliers start: 12 outliers final: 6 residues processed: 73 average time/residue: 0.1763 time to fit residues: 15.3704 Evaluate side-chains 61 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 545 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3390 Z= 0.230 Angle : 0.667 5.966 4644 Z= 0.348 Chirality : 0.045 0.149 544 Planarity : 0.004 0.033 598 Dihedral : 4.180 15.705 454 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.70 % Allowed : 19.05 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.40), residues: 420 helix: -0.60 (0.76), residues: 44 sheet: 1.48 (0.39), residues: 160 loop : -1.80 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 528 HIS 0.005 0.001 HIS B 518 PHE 0.018 0.003 PHE A 479 TYR 0.018 0.002 TYR A 500 ARG 0.003 0.000 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: B 489 MET cc_start: 0.7923 (tpp) cc_final: 0.7317 (mmm) REVERT: A 367 CYS cc_start: 0.7611 (p) cc_final: 0.7189 (p) REVERT: A 468 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7476 (pt0) REVERT: A 489 MET cc_start: 0.8026 (tpp) cc_final: 0.7351 (mmm) REVERT: A 506 MET cc_start: 0.6801 (mmm) cc_final: 0.6012 (ptp) REVERT: A 536 CYS cc_start: 0.8282 (p) cc_final: 0.8063 (t) outliers start: 14 outliers final: 8 residues processed: 69 average time/residue: 0.2110 time to fit residues: 17.1271 Evaluate side-chains 65 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 545 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 518 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3390 Z= 0.267 Angle : 0.686 7.942 4644 Z= 0.354 Chirality : 0.045 0.147 544 Planarity : 0.005 0.035 598 Dihedral : 4.368 16.729 454 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.44 % Allowed : 19.58 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.41), residues: 420 helix: -0.68 (0.80), residues: 44 sheet: 1.55 (0.40), residues: 160 loop : -1.83 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 528 HIS 0.005 0.001 HIS B 518 PHE 0.019 0.003 PHE B 479 TYR 0.016 0.002 TYR A 500 ARG 0.005 0.000 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: B 489 MET cc_start: 0.7976 (tpp) cc_final: 0.7336 (mmm) REVERT: B 506 MET cc_start: 0.6679 (mmm) cc_final: 0.5665 (mtm) REVERT: A 367 CYS cc_start: 0.7626 (p) cc_final: 0.6890 (p) REVERT: A 468 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7475 (pt0) REVERT: A 489 MET cc_start: 0.7968 (tpp) cc_final: 0.7611 (mtp) REVERT: A 536 CYS cc_start: 0.8426 (p) cc_final: 0.8163 (t) outliers start: 13 outliers final: 7 residues processed: 71 average time/residue: 0.1978 time to fit residues: 16.5649 Evaluate side-chains 67 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 545 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7568 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3390 Z= 0.253 Angle : 0.697 8.248 4644 Z= 0.357 Chirality : 0.045 0.149 544 Planarity : 0.005 0.036 598 Dihedral : 4.493 17.010 454 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.65 % Allowed : 20.90 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.41), residues: 420 helix: -0.88 (0.79), residues: 44 sheet: 1.53 (0.40), residues: 160 loop : -1.87 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 382 HIS 0.006 0.001 HIS A 518 PHE 0.017 0.002 PHE A 479 TYR 0.014 0.001 TYR A 500 ARG 0.002 0.000 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.355 Fit side-chains REVERT: B 506 MET cc_start: 0.6772 (mmm) cc_final: 0.5735 (mtm) REVERT: A 468 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7479 (pt0) REVERT: A 489 MET cc_start: 0.7963 (tpp) cc_final: 0.7651 (mtp) REVERT: A 506 MET cc_start: 0.6758 (mmm) cc_final: 0.5697 (mtm) REVERT: A 536 CYS cc_start: 0.8474 (p) cc_final: 0.8188 (t) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 0.1891 time to fit residues: 15.4239 Evaluate side-chains 65 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 545 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3390 Z= 0.190 Angle : 0.662 7.077 4644 Z= 0.341 Chirality : 0.045 0.234 544 Planarity : 0.004 0.035 598 Dihedral : 4.329 17.309 454 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.91 % Allowed : 21.43 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.41), residues: 420 helix: -1.00 (0.76), residues: 44 sheet: 1.56 (0.40), residues: 160 loop : -1.79 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 382 HIS 0.006 0.001 HIS B 518 PHE 0.011 0.002 PHE A 479 TYR 0.012 0.001 TYR B 500 ARG 0.002 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.406 Fit side-chains REVERT: B 438 LYS cc_start: 0.8186 (mmtp) cc_final: 0.7952 (mmtt) REVERT: B 506 MET cc_start: 0.6675 (mmm) cc_final: 0.5719 (mtm) REVERT: A 350 ILE cc_start: 0.9074 (mp) cc_final: 0.8846 (tp) REVERT: A 489 MET cc_start: 0.7928 (tpp) cc_final: 0.7628 (mtp) REVERT: A 506 MET cc_start: 0.6682 (mmm) cc_final: 0.5618 (mtm) REVERT: A 536 CYS cc_start: 0.8483 (p) cc_final: 0.8276 (t) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.1377 time to fit residues: 11.9133 Evaluate side-chains 65 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 547 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 0.0070 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 GLN ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3390 Z= 0.196 Angle : 0.659 6.642 4644 Z= 0.340 Chirality : 0.044 0.158 544 Planarity : 0.004 0.034 598 Dihedral : 4.362 17.155 454 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.70 % Allowed : 20.63 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.41), residues: 420 helix: -1.17 (0.73), residues: 44 sheet: 1.56 (0.40), residues: 160 loop : -1.74 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 382 HIS 0.006 0.001 HIS B 518 PHE 0.013 0.002 PHE A 479 TYR 0.012 0.001 TYR B 500 ARG 0.003 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.391 Fit side-chains REVERT: B 438 LYS cc_start: 0.8049 (mmtp) cc_final: 0.7770 (mmtt) REVERT: B 506 MET cc_start: 0.6658 (mmm) cc_final: 0.5728 (mtm) REVERT: A 350 ILE cc_start: 0.9051 (mp) cc_final: 0.8824 (tp) REVERT: A 489 MET cc_start: 0.7883 (tpp) cc_final: 0.7549 (mtp) REVERT: A 506 MET cc_start: 0.6654 (mmm) cc_final: 0.5671 (mtm) REVERT: A 536 CYS cc_start: 0.8514 (p) cc_final: 0.8303 (t) outliers start: 14 outliers final: 8 residues processed: 67 average time/residue: 0.1427 time to fit residues: 11.9395 Evaluate side-chains 64 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 547 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.0170 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3390 Z= 0.214 Angle : 0.661 6.666 4644 Z= 0.344 Chirality : 0.045 0.160 544 Planarity : 0.005 0.037 598 Dihedral : 4.506 16.974 454 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 2.65 % Allowed : 21.16 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.41), residues: 420 helix: -1.23 (0.73), residues: 44 sheet: 1.68 (0.41), residues: 160 loop : -1.74 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 382 HIS 0.010 0.001 HIS B 518 PHE 0.013 0.002 PHE A 479 TYR 0.011 0.001 TYR B 500 ARG 0.003 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.402 Fit side-chains REVERT: B 438 LYS cc_start: 0.8024 (mmtp) cc_final: 0.7690 (mmtt) REVERT: B 439 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7876 (tm-30) REVERT: B 506 MET cc_start: 0.6709 (mmm) cc_final: 0.5734 (mtm) REVERT: A 350 ILE cc_start: 0.9094 (mp) cc_final: 0.8842 (tp) REVERT: A 489 MET cc_start: 0.7899 (tpp) cc_final: 0.7574 (mtp) REVERT: A 506 MET cc_start: 0.6673 (mmm) cc_final: 0.5720 (mtm) REVERT: A 536 CYS cc_start: 0.8526 (p) cc_final: 0.8291 (t) outliers start: 10 outliers final: 6 residues processed: 67 average time/residue: 0.1769 time to fit residues: 14.2958 Evaluate side-chains 67 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 547 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.0870 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.0470 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.0670 chunk 6 optimal weight: 4.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3390 Z= 0.196 Angle : 0.680 7.441 4644 Z= 0.352 Chirality : 0.045 0.155 544 Planarity : 0.004 0.035 598 Dihedral : 4.523 17.219 454 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 1.85 % Allowed : 22.49 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.41), residues: 420 helix: -1.38 (0.69), residues: 44 sheet: 1.74 (0.41), residues: 160 loop : -1.73 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 382 HIS 0.011 0.001 HIS B 518 PHE 0.009 0.001 PHE A 479 TYR 0.019 0.001 TYR B 500 ARG 0.002 0.000 ARG A 491 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: B 382 TRP cc_start: 0.7103 (m100) cc_final: 0.6502 (m-10) REVERT: B 439 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7869 (tm-30) REVERT: A 350 ILE cc_start: 0.9041 (mp) cc_final: 0.8822 (tp) REVERT: A 489 MET cc_start: 0.7893 (tpp) cc_final: 0.7582 (mtp) REVERT: A 506 MET cc_start: 0.6637 (mmm) cc_final: 0.5749 (mtm) REVERT: A 536 CYS cc_start: 0.8527 (p) cc_final: 0.8262 (t) outliers start: 7 outliers final: 6 residues processed: 64 average time/residue: 0.1518 time to fit residues: 12.0317 Evaluate side-chains 62 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 547 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 HIS ** 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 = 0.4257 r_free = 0.4257 target = 0.179400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129052 restraints weight = 5133.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.133679 restraints weight = 2940.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136614 restraints weight = 2116.532| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3390 Z= 0.221 Angle : 0.730 15.890 4644 Z= 0.368 Chirality : 0.045 0.147 544 Planarity : 0.004 0.034 598 Dihedral : 4.510 17.788 454 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.59 % Allowed : 22.75 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.41), residues: 420 helix: -1.39 (0.70), residues: 46 sheet: 1.76 (0.41), residues: 160 loop : -1.73 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 382 HIS 0.010 0.001 HIS B 518 PHE 0.013 0.002 PHE A 479 TYR 0.021 0.001 TYR B 500 ARG 0.002 0.000 ARG A 491 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1226.24 seconds wall clock time: 22 minutes 41.97 seconds (1361.97 seconds total)