Starting phenix.real_space_refine on Fri Aug 2 15:13:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdo_13922/08_2024/7qdo_13922.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdo_13922/08_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_13922/08_2024/7qdo_13922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdo_13922/08_2024/7qdo_13922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdo_13922/08_2024/7qdo_13922.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdo_13922/08_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 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-dev-5409/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: 2.56, per 1000 atoms: 0.77 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: 1.11 Conformation dependent library (CDL) restraints added in 580.4 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: 0.83 Time building geometry restraints manager: 1.18 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 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 nonbonded pdb=" OG1 THR A 363 " pdb=" O ILE A 413 " model vdw 2.270 3.040 nonbonded pdb=" O ASP B 417 " pdb=" OG SER B 420 " model vdw 2.478 3.040 ... (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 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: 1.000 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.370 Find NCS groups from input model: 0.070 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- 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 : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1655 time to fit residues: 19.1058 Evaluate side-chains 67 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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** ** 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: 0.7403 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3390 Z= 0.220 Angle : 0.697 6.220 4644 Z= 0.366 Chirality : 0.047 0.161 544 Planarity : 0.005 0.036 598 Dihedral : 4.268 16.269 454 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.50 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: -0.38 (0.41), residues: 420 helix: -0.48 (0.74), residues: 44 sheet: 1.38 (0.39), residues: 174 loop : -1.79 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 528 HIS 0.007 0.001 HIS A 518 PHE 0.017 0.002 PHE B 479 TYR 0.004 0.001 TYR B 534 ARG 0.004 0.000 ARG B 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 86 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.368 Fit side-chains REVERT: B 417 ASP cc_start: 0.8212 (p0) cc_final: 0.7912 (p0) REVERT: B 506 MET cc_start: 0.6605 (mmm) cc_final: 0.6098 (ptt) REVERT: A 506 MET cc_start: 0.6616 (mmm) cc_final: 0.6096 (ptt) outliers start: 7 outliers final: 6 residues processed: 82 average time/residue: 0.1701 time to fit residues: 16.7167 Evaluate side-chains 60 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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: 2.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7450 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3390 Z= 0.203 Angle : 0.664 5.818 4644 Z= 0.348 Chirality : 0.045 0.153 544 Planarity : 0.004 0.031 598 Dihedral : 4.265 17.478 454 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.91 % Allowed : 14.29 % Favored : 82.80 % 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: -0.54 (0.40), residues: 420 helix: -0.35 (0.75), residues: 44 sheet: 1.37 (0.40), residues: 160 loop : -1.84 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 528 HIS 0.009 0.001 HIS B 518 PHE 0.016 0.002 PHE B 479 TYR 0.016 0.001 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 73 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.375 Fit side-chains REVERT: B 506 MET cc_start: 0.6765 (mmm) cc_final: 0.6110 (ptt) REVERT: A 506 MET cc_start: 0.6661 (mmm) cc_final: 0.6038 (ptt) outliers start: 11 outliers final: 7 residues processed: 66 average time/residue: 0.1693 time to fit residues: 13.4954 Evaluate side-chains 59 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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** A 518 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3390 Z= 0.223 Angle : 0.665 5.899 4644 Z= 0.347 Chirality : 0.044 0.149 544 Planarity : 0.004 0.034 598 Dihedral : 4.306 17.476 454 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.65 % Allowed : 19.05 % 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: -0.58 (0.40), residues: 420 helix: -0.57 (0.76), residues: 44 sheet: 1.36 (0.40), residues: 160 loop : -1.83 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 528 HIS 0.007 0.001 HIS B 518 PHE 0.020 0.002 PHE A 405 TYR 0.010 0.002 TYR B 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 72 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.380 Fit side-chains REVERT: B 489 MET cc_start: 0.7903 (tpp) cc_final: 0.7313 (mmm) REVERT: B 506 MET cc_start: 0.6780 (mmm) cc_final: 0.5994 (ptp) REVERT: A 489 MET cc_start: 0.7985 (tpp) cc_final: 0.7350 (mmm) REVERT: A 506 MET cc_start: 0.6740 (mmm) cc_final: 0.5986 (ptp) outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.2202 time to fit residues: 16.6582 Evaluate side-chains 59 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.7614 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 3390 Z= 0.406 Angle : 0.777 7.423 4644 Z= 0.407 Chirality : 0.047 0.147 544 Planarity : 0.005 0.037 598 Dihedral : 4.801 19.575 454 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 4.76 % Allowed : 17.46 % Favored : 77.78 % 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: -0.61 (0.42), residues: 420 helix: -0.56 (0.82), residues: 44 sheet: 1.34 (0.42), residues: 160 loop : -1.85 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 528 HIS 0.011 0.002 HIS B 518 PHE 0.026 0.004 PHE A 479 TYR 0.012 0.002 TYR B 455 ARG 0.003 0.000 ARG B 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 82 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 0.387 Fit side-chains REVERT: B 489 MET cc_start: 0.7948 (tpp) cc_final: 0.7589 (mtp) REVERT: A 489 MET cc_start: 0.7913 (tpp) cc_final: 0.7565 (mtp) outliers start: 18 outliers final: 11 residues processed: 72 average time/residue: 0.1862 time to fit residues: 15.9618 Evaluate side-chains 67 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 442 SER 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 442 SER Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 520 ILE 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: 2.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7563 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3390 Z= 0.232 Angle : 0.721 8.660 4644 Z= 0.371 Chirality : 0.046 0.146 544 Planarity : 0.005 0.038 598 Dihedral : 4.756 18.992 454 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 2.65 % Allowed : 19.84 % Favored : 77.51 % 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: -0.65 (0.42), residues: 420 helix: -0.66 (0.80), residues: 44 sheet: 1.34 (0.41), residues: 160 loop : -1.89 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 528 HIS 0.012 0.002 HIS B 518 PHE 0.014 0.002 PHE B 479 TYR 0.011 0.001 TYR B 500 ARG 0.004 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 75 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.377 Fit side-chains REVERT: B 439 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7659 (mp10) REVERT: B 489 MET cc_start: 0.7913 (tpp) cc_final: 0.7519 (mtp) REVERT: B 506 MET cc_start: 0.6700 (mmm) cc_final: 0.5708 (mtm) REVERT: A 439 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7656 (mp10) REVERT: A 506 MET cc_start: 0.6608 (mmm) cc_final: 0.5669 (mtm) outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 0.1792 time to fit residues: 14.3618 Evaluate side-chains 68 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 0.0030 chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.5368 ------------------------------------------------------------------------------- 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: 0.7518 moved from start: 0.3995 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= 0.182 Angle : 0.657 5.723 4644 Z= 0.341 Chirality : 0.045 0.145 544 Planarity : 0.004 0.035 598 Dihedral : 4.544 18.624 454 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.91 % Allowed : 19.84 % 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: -0.64 (0.41), residues: 420 helix: -1.01 (0.75), residues: 44 sheet: 1.62 (0.41), residues: 152 loop : -1.92 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 382 HIS 0.009 0.001 HIS B 518 PHE 0.009 0.002 PHE A 479 TYR 0.004 0.001 TYR B 534 ARG 0.004 0.000 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 73 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.386 Fit side-chains REVERT: B 350 ILE cc_start: 0.9023 (mp) cc_final: 0.8817 (tp) REVERT: B 489 MET cc_start: 0.7942 (tpp) cc_final: 0.7549 (mtp) REVERT: A 506 MET cc_start: 0.6417 (mmm) cc_final: 0.5518 (mtm) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 0.1660 time to fit residues: 13.5660 Evaluate side-chains 61 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.7495 moved from start: 0.4209 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= 0.190 Angle : 0.733 16.600 4644 Z= 0.365 Chirality : 0.045 0.201 544 Planarity : 0.004 0.034 598 Dihedral : 4.422 18.066 454 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % 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: -0.57 (0.41), residues: 420 helix: -1.22 (0.72), residues: 44 sheet: 1.58 (0.41), residues: 160 loop : -1.86 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 382 HIS 0.009 0.001 HIS B 518 PHE 0.009 0.002 PHE A 479 TYR 0.013 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: 10 poor density : 62 time to evaluate : 0.424 Fit side-chains REVERT: B 439 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7659 (mp10) REVERT: B 467 ARG cc_start: 0.7744 (mmt180) cc_final: 0.7420 (mpt-90) REVERT: B 506 MET cc_start: 0.5996 (mmm) cc_final: 0.5331 (mtm) REVERT: A 439 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7665 (mp10) REVERT: A 506 MET cc_start: 0.6493 (mmm) cc_final: 0.5566 (mtm) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 0.1347 time to fit residues: 11.8344 Evaluate side-chains 61 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.0470 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- 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: 0.7548 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 : 0.004 0.038 3390 Z= 0.246 Angle : 0.738 15.466 4644 Z= 0.373 Chirality : 0.046 0.154 544 Planarity : 0.005 0.033 598 Dihedral : 4.616 18.693 454 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 2.65 % Allowed : 21.96 % 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: -0.51 (0.42), residues: 420 helix: -1.04 (0.76), residues: 44 sheet: 1.67 (0.41), residues: 160 loop : -1.90 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 382 HIS 0.009 0.001 HIS B 518 PHE 0.016 0.002 PHE A 479 TYR 0.010 0.001 TYR A 500 ARG 0.003 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 67 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: B 467 ARG cc_start: 0.7804 (mmt180) cc_final: 0.7432 (mpt-90) REVERT: B 506 MET cc_start: 0.6170 (mmm) cc_final: 0.5398 (mtm) REVERT: A 506 MET cc_start: 0.6583 (mmm) cc_final: 0.5680 (mtm) outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 0.1541 time to fit residues: 11.7172 Evaluate side-chains 61 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain A residue 350 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.9338 > 50: distance: 16 - 129: 30.845 distance: 19 - 126: 18.157 distance: 49 - 56: 6.234 distance: 56 - 57: 9.674 distance: 57 - 58: 16.303 distance: 57 - 60: 27.449 distance: 58 - 59: 23.467 distance: 58 - 64: 47.025 distance: 60 - 61: 23.802 distance: 61 - 62: 15.804 distance: 61 - 63: 31.265 distance: 64 - 65: 19.486 distance: 65 - 66: 7.711 distance: 65 - 68: 34.441 distance: 66 - 67: 11.494 distance: 66 - 72: 17.340 distance: 68 - 69: 5.586 distance: 69 - 70: 22.878 distance: 69 - 71: 15.268 distance: 72 - 73: 14.109 distance: 73 - 74: 38.676 distance: 73 - 76: 18.825 distance: 74 - 75: 12.026 distance: 74 - 80: 42.368 distance: 77 - 78: 33.047 distance: 77 - 79: 41.315 distance: 81 - 82: 9.490 distance: 81 - 84: 16.298 distance: 82 - 83: 32.785 distance: 82 - 91: 54.020 distance: 84 - 85: 27.814 distance: 85 - 86: 17.477 distance: 86 - 87: 11.871 distance: 87 - 88: 41.040 distance: 88 - 89: 7.650 distance: 88 - 90: 6.504 distance: 91 - 92: 37.604 distance: 92 - 93: 26.956 distance: 92 - 95: 35.831 distance: 93 - 94: 19.845 distance: 93 - 100: 40.492 distance: 95 - 96: 5.358 distance: 96 - 97: 24.797 distance: 97 - 98: 34.237 distance: 97 - 99: 14.862 distance: 100 - 101: 5.474 distance: 101 - 102: 19.951 distance: 101 - 104: 32.547 distance: 102 - 103: 7.933 distance: 102 - 106: 47.695 distance: 104 - 105: 11.441 distance: 106 - 107: 25.186 distance: 106 - 173: 30.898 distance: 107 - 108: 23.639 distance: 107 - 110: 18.478 distance: 108 - 109: 7.685 distance: 108 - 111: 26.459 distance: 109 - 170: 14.793 distance: 111 - 112: 15.298 distance: 112 - 113: 10.365 distance: 112 - 115: 3.827 distance: 113 - 114: 18.910 distance: 113 - 118: 38.750 distance: 115 - 116: 28.981 distance: 115 - 117: 35.569 distance: 118 - 161: 25.802 distance: 119 - 120: 31.266 distance: 119 - 122: 22.025 distance: 120 - 121: 36.112 distance: 120 - 126: 21.322 distance: 121 - 158: 30.015 distance: 122 - 123: 21.248 distance: 122 - 124: 10.733 distance: 123 - 125: 23.974 distance: 126 - 127: 4.508 distance: 127 - 128: 10.753 distance: 127 - 130: 28.045 distance: 128 - 129: 15.469 distance: 128 - 133: 22.129 distance: 130 - 131: 21.973 distance: 130 - 132: 15.561