Starting phenix.real_space_refine on Thu Dec 7 17:55:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdo_13922/12_2023/7qdo_13922.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdo_13922/12_2023/7qdo_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_13922/12_2023/7qdo_13922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdo_13922/12_2023/7qdo_13922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdo_13922/12_2023/7qdo_13922.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdo_13922/12_2023/7qdo_13922.pdb" } 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 Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 376": "OD1" <-> "OD2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B ASP 417": "OD1" <-> "OD2" Residue "B ASP 453": "OD1" <-> "OD2" Residue "B ASP 483": "OD1" <-> "OD2" Residue "B TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B GLU 532": "OE1" <-> "OE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "A ASP 453": "OD1" <-> "OD2" Residue "A ASP 483": "OD1" <-> "OD2" Residue "A TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A GLU 532": "OE1" <-> "OE2" Residue "A GLU 541": "OE1" <-> "OE2" Residue "A GLU 549": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3304 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" 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} 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} Time building chain proxies: 2.23, per 1000 atoms: 0.67 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=4, 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 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.04 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.04 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: 1.29 Conformation dependent library (CDL) restraints added in 566.4 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: 0.45 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: 0.86 Time building geometry restraints manager: 1.39 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: 101.17 - 107.78: 198 107.78 - 114.40: 1950 114.40 - 121.01: 1375 121.01 - 127.62: 1075 127.62 - 134.23: 46 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: 1874 15.93 - 31.87: 144 31.87 - 47.80: 36 47.80 - 63.73: 0 63.73 - 79.66: 2 Dihedral angle restraints: 2056 sinusoidal: 808 harmonic: 1248 Sorted by residual: dihedral pdb=" CB CYS A 367 " pdb=" SG CYS A 367 " pdb=" SG CYS A 426 " pdb=" CB CYS A 426 " ideal model delta sinusoidal sigma weight residual 93.00 137.29 -44.29 1 1.00e+01 1.00e-02 2.73e+01 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 ... (remaining 2053 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: 2.22 - 2.76: 401 2.76 - 3.29: 3134 3.29 - 3.83: 5189 3.83 - 4.36: 5766 4.36 - 4.90: 10067 Nonbonded interactions: 24557 Sorted by model distance: nonbonded pdb=" OD1 ASP A 553 " pdb=" OG1 THR A 556 " model vdw 2.223 2.440 nonbonded pdb=" OD1 ASP B 553 " pdb=" OG1 THR B 556 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR B 363 " pdb=" O ILE B 413 " model vdw 2.270 2.440 nonbonded pdb=" OG1 THR A 363 " pdb=" O ILE A 413 " model vdw 2.270 2.440 nonbonded pdb=" O ASP B 417 " pdb=" OG SER B 420 " model vdw 2.478 2.440 ... (remaining 24552 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.780 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: 0.000 Extract box with map and model: 3.440 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.670 Find NCS groups from input model: 0.160 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.970 ------------------------------------------------------------------------------- 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= 0.344 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 : 2.223 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 : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1710 time to fit residues: 19.7437 Evaluate side-chains 67 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5354 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3390 Z= 0.220 Angle : 0.668 6.422 4644 Z= 0.350 Chirality : 0.045 0.155 544 Planarity : 0.005 0.031 598 Dihedral : 4.268 16.911 454 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 1.59 % Allowed : 10.58 % Favored : 87.83 % 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 (0.41), residues: 420 helix: -0.96 (0.76), residues: 44 sheet: 1.24 (0.40), residues: 174 loop : -1.73 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 488 HIS 0.008 0.002 HIS A 518 PHE 0.018 0.002 PHE B 479 TYR 0.005 0.001 TYR B 534 ARG 0.004 0.000 ARG B 443 *********************** 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 84 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 81 average time/residue: 0.1809 time to fit residues: 17.5008 Evaluate side-chains 60 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1456 time to fit residues: 1.3965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0060 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.0050 chunk 13 optimal weight: 0.0570 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 overall best weight: 0.2728 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3390 Z= 0.150 Angle : 0.606 5.306 4644 Z= 0.313 Chirality : 0.043 0.144 544 Planarity : 0.004 0.028 598 Dihedral : 4.053 14.608 454 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.85 % Allowed : 13.23 % Favored : 84.92 % 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: -0.69 (0.40), residues: 420 helix: -1.06 (0.77), residues: 44 sheet: 1.24 (0.39), residues: 160 loop : -1.77 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 528 HIS 0.006 0.001 HIS B 518 PHE 0.019 0.002 PHE A 516 TYR 0.012 0.001 TYR B 500 ARG 0.003 0.000 ARG A 443 *********************** 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 79 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 75 average time/residue: 0.1981 time to fit residues: 17.9049 Evaluate side-chains 58 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0489 time to fit residues: 0.6409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3390 Z= 0.287 Angle : 0.683 6.554 4644 Z= 0.357 Chirality : 0.045 0.187 544 Planarity : 0.004 0.031 598 Dihedral : 4.493 16.470 454 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.91 % Allowed : 18.78 % Favored : 78.31 % 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: -0.39 (0.41), residues: 420 helix: -0.14 (0.82), residues: 44 sheet: 1.29 (0.39), residues: 174 loop : -1.80 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 528 HIS 0.006 0.001 HIS B 518 PHE 0.023 0.003 PHE B 479 TYR 0.012 0.002 TYR A 455 ARG 0.005 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 74 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 69 average time/residue: 0.2223 time to fit residues: 17.8838 Evaluate side-chains 66 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1071 time to fit residues: 1.4528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 GLN A 518 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3390 Z= 0.352 Angle : 0.725 6.733 4644 Z= 0.378 Chirality : 0.047 0.188 544 Planarity : 0.005 0.037 598 Dihedral : 4.741 17.060 454 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.12 % Allowed : 20.63 % 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: -0.69 (0.41), residues: 420 helix: -0.25 (0.82), residues: 44 sheet: 1.19 (0.40), residues: 160 loop : -1.91 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 528 HIS 0.005 0.001 HIS A 393 PHE 0.023 0.003 PHE A 479 TYR 0.011 0.002 TYR B 455 ARG 0.003 0.001 ARG A 514 *********************** 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 76 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 73 average time/residue: 0.2140 time to fit residues: 18.2049 Evaluate side-chains 59 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0386 time to fit residues: 0.7447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.0870 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.1962 ------------------------------------------------------------------------------- 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** B 518 HIS ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3390 Z= 0.269 Angle : 0.688 6.126 4644 Z= 0.355 Chirality : 0.046 0.170 544 Planarity : 0.005 0.036 598 Dihedral : 4.668 19.454 454 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.38 % Allowed : 20.37 % 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: -0.68 (0.41), residues: 420 helix: -0.33 (0.81), residues: 44 sheet: 1.15 (0.39), residues: 160 loop : -1.84 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 528 HIS 0.004 0.001 HIS A 518 PHE 0.017 0.002 PHE A 479 TYR 0.010 0.002 TYR B 500 ARG 0.007 0.001 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 72 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 0.1859 time to fit residues: 14.7123 Evaluate side-chains 66 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.430 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0379 time to fit residues: 0.8990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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** B 487 GLN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7568 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3390 Z= 0.256 Angle : 0.709 7.469 4644 Z= 0.363 Chirality : 0.045 0.173 544 Planarity : 0.005 0.036 598 Dihedral : 4.612 17.764 454 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 1.59 % Allowed : 23.28 % Favored : 75.13 % 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: -0.68 (0.41), residues: 420 helix: -0.30 (0.82), residues: 44 sheet: 1.17 (0.40), residues: 160 loop : -1.87 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 528 HIS 0.009 0.002 HIS A 518 PHE 0.017 0.002 PHE B 479 TYR 0.019 0.002 TYR B 500 ARG 0.005 0.001 ARG B 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 64 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 62 average time/residue: 0.1574 time to fit residues: 12.0134 Evaluate side-chains 61 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0361 time to fit residues: 0.6318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 36 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.0030 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 GLN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4254 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= 0.178 Angle : 0.652 6.036 4644 Z= 0.332 Chirality : 0.044 0.142 544 Planarity : 0.004 0.035 598 Dihedral : 4.346 15.982 454 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.38 % Allowed : 21.16 % 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: -0.62 (0.41), residues: 420 helix: -0.39 (0.80), residues: 44 sheet: 1.25 (0.40), residues: 160 loop : -1.82 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 382 HIS 0.004 0.001 HIS B 518 PHE 0.010 0.002 PHE A 516 TYR 0.019 0.001 TYR B 500 ARG 0.004 0.000 ARG B 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 72 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 0.1226 time to fit residues: 10.5509 Evaluate side-chains 65 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0380 time to fit residues: 0.8916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.0020 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 0.0770 chunk 25 optimal weight: 0.0570 overall best weight: 0.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 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: 0.7484 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3390 Z= 0.182 Angle : 0.654 5.926 4644 Z= 0.335 Chirality : 0.045 0.139 544 Planarity : 0.005 0.034 598 Dihedral : 4.325 14.617 454 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.32 % Allowed : 21.96 % Favored : 76.72 % 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: -0.60 (0.41), residues: 420 helix: -0.44 (0.80), residues: 44 sheet: 1.29 (0.40), residues: 160 loop : -1.82 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP B 382 HIS 0.005 0.001 HIS A 518 PHE 0.013 0.002 PHE A 516 TYR 0.017 0.001 TYR B 500 ARG 0.004 0.000 ARG B 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 64 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 63 average time/residue: 0.1445 time to fit residues: 11.4561 Evaluate side-chains 57 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0373 time to fit residues: 0.6210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.0770 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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** ** 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: 0.7505 moved from start: 0.4369 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= 0.212 Angle : 0.685 6.857 4644 Z= 0.356 Chirality : 0.045 0.144 544 Planarity : 0.005 0.040 598 Dihedral : 4.471 16.061 454 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.53 % Allowed : 24.07 % Favored : 75.40 % 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: -0.57 (0.41), residues: 420 helix: -0.41 (0.81), residues: 44 sheet: 1.32 (0.40), residues: 160 loop : -1.82 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.007 TRP B 382 HIS 0.006 0.001 HIS A 518 PHE 0.015 0.002 PHE A 516 TYR 0.019 0.002 TYR B 500 ARG 0.003 0.000 ARG B 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 60 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 60 average time/residue: 0.1699 time to fit residues: 12.6203 Evaluate side-chains 59 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2718 time to fit residues: 1.1178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 0.0470 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4221 r_free = 0.4221 target = 0.177579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.128103 restraints weight = 5084.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133072 restraints weight = 2752.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136348 restraints weight = 1890.119| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3390 Z= 0.248 Angle : 0.692 6.112 4644 Z= 0.355 Chirality : 0.045 0.142 544 Planarity : 0.005 0.033 598 Dihedral : 4.515 16.281 454 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 1.59 % Allowed : 25.13 % Favored : 73.28 % 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: -0.62 (0.41), residues: 420 helix: -0.32 (0.83), residues: 44 sheet: 1.27 (0.41), residues: 160 loop : -1.87 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP B 382 HIS 0.005 0.001 HIS A 518 PHE 0.015 0.002 PHE B 479 TYR 0.022 0.002 TYR A 500 ARG 0.003 0.000 ARG B 491 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1216.52 seconds wall clock time: 22 minutes 43.13 seconds (1363.13 seconds total)