Starting phenix.real_space_refine on Wed Jan 17 13:10:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtg_32785/01_2024/7wtg_32785.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtg_32785/01_2024/7wtg_32785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtg_32785/01_2024/7wtg_32785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtg_32785/01_2024/7wtg_32785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtg_32785/01_2024/7wtg_32785.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtg_32785/01_2024/7wtg_32785.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 17 5.16 5 C 2107 2.51 5 N 563 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 420": "OD1" <-> "OD2" Residue "E ASP 442": "OD1" <-> "OD2" Residue "E GLU 465": "OE1" <-> "OE2" Residue "E TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 3318 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Time building chain proxies: 2.26, per 1000 atoms: 0.68 Number of scatterers: 3318 At special positions: 0 Unit cell: (60.32, 64.48, 115.44, 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 17 16.00 O 631 8.00 N 563 7.00 C 2107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 616.2 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 8 sheets defined 5.2% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.596A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 403 through 405 No H-bonds generated for 'chain 'E' and resid 403 through 405' Processing helix chain 'E' and resid 406 through 411 removed outlier: 3.762A pdb=" N ILE E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA E 411 " --> pdb=" O VAL E 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 406 through 411' Processing sheet with id=AA1, first strand: chain 'E' and resid 356 through 358 removed outlier: 4.408A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.513A pdb=" N ASN H 59 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA H 33 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU H 99 " --> pdb=" O ALA H 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 48 removed outlier: 7.248A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 45 through 48 removed outlier: 7.248A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 180 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: 0.78 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1064 1.35 - 1.47: 930 1.47 - 1.60: 1389 1.60 - 1.73: 0 1.73 - 1.85: 21 Bond restraints: 3404 Sorted by residual: bond pdb=" N VAL E 445 " pdb=" CA VAL E 445 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.77e+00 bond pdb=" N LYS E 444 " pdb=" CA LYS E 444 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.21e-02 6.83e+03 7.14e+00 bond pdb=" N GLY E 447 " pdb=" CA GLY E 447 " ideal model delta sigma weight residual 1.450 1.476 -0.025 1.01e-02 9.80e+03 6.18e+00 bond pdb=" N SER E 446 " pdb=" CA SER E 446 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.66e+00 bond pdb=" CA VAL L 58 " pdb=" CB VAL L 58 " ideal model delta sigma weight residual 1.537 1.563 -0.026 1.29e-02 6.01e+03 4.06e+00 ... (remaining 3399 not shown) Histogram of bond angle deviations from ideal: 97.47 - 104.80: 62 104.80 - 112.14: 1497 112.14 - 119.47: 1237 119.47 - 126.81: 1775 126.81 - 134.15: 49 Bond angle restraints: 4620 Sorted by residual: angle pdb=" C ILE E 410 " pdb=" N ALA E 411 " pdb=" CA ALA E 411 " ideal model delta sigma weight residual 120.60 127.40 -6.80 1.53e+00 4.27e-01 1.98e+01 angle pdb=" C GLY H 113 " pdb=" N MET H 114 " pdb=" CA MET H 114 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" N TYR L 94 " pdb=" CA TYR L 94 " pdb=" C TYR L 94 " ideal model delta sigma weight residual 109.81 119.12 -9.31 2.21e+00 2.05e-01 1.77e+01 angle pdb=" CA GLY E 447 " pdb=" C GLY E 447 " pdb=" O GLY E 447 " ideal model delta sigma weight residual 122.05 118.00 4.05 1.00e+00 1.00e+00 1.64e+01 angle pdb=" C GLN H 62 " pdb=" N LYS H 63 " pdb=" CA LYS H 63 " ideal model delta sigma weight residual 121.54 128.80 -7.26 1.91e+00 2.74e-01 1.44e+01 ... (remaining 4615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1798 17.95 - 35.90: 181 35.90 - 53.84: 29 53.84 - 71.79: 4 71.79 - 89.74: 5 Dihedral angle restraints: 2017 sinusoidal: 790 harmonic: 1227 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 165.13 -72.13 1 1.00e+01 1.00e-02 6.65e+01 dihedral pdb=" CA CYS E 361 " pdb=" C CYS E 361 " pdb=" N VAL E 362 " pdb=" CA VAL E 362 " ideal model delta harmonic sigma weight residual 180.00 141.00 39.00 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CA PRO E 337 " pdb=" C PRO E 337 " pdb=" N PHE E 338 " pdb=" CA PHE E 338 " ideal model delta harmonic sigma weight residual 180.00 149.52 30.48 0 5.00e+00 4.00e-02 3.72e+01 ... (remaining 2014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 349 0.058 - 0.116: 95 0.116 - 0.174: 34 0.174 - 0.233: 8 0.233 - 0.291: 4 Chirality restraints: 490 Sorted by residual: chirality pdb=" CB THR L 85 " pdb=" CA THR L 85 " pdb=" OG1 THR L 85 " pdb=" CG2 THR L 85 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB VAL L 58 " pdb=" CA VAL L 58 " pdb=" CG1 VAL L 58 " pdb=" CG2 VAL L 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ASN E 354 " pdb=" N ASN E 354 " pdb=" C ASN E 354 " pdb=" CB ASN E 354 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 487 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 462 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO E 463 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO E 463 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 463 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 453 " 0.022 2.00e-02 2.50e+03 2.12e-02 9.01e+00 pdb=" CG TYR E 453 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR E 453 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR E 453 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 453 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR E 453 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR E 453 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 453 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO L 59 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.041 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 922 2.82 - 3.34: 2655 3.34 - 3.86: 5232 3.86 - 4.38: 5684 4.38 - 4.90: 10127 Nonbonded interactions: 24620 Sorted by model distance: nonbonded pdb=" O SER L 60 " pdb=" OG SER L 60 " model vdw 2.297 2.440 nonbonded pdb=" O ILE L 2 " pdb=" OG1 THR L 97 " model vdw 2.349 2.440 nonbonded pdb=" NH2 ARG H 67 " pdb=" OD2 ASP H 90 " model vdw 2.364 2.520 nonbonded pdb=" OD2 ASP E 398 " pdb=" OH TYR E 423 " model vdw 2.396 2.440 nonbonded pdb=" OG1 THR L 85 " pdb=" O GLY L 101 " model vdw 2.398 2.440 ... (remaining 24615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.340 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: 8.850 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.470 Find NCS groups from input model: 0.090 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 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 : 0.006 0.050 3404 Z= 0.390 Angle : 1.201 11.712 4620 Z= 0.644 Chirality : 0.069 0.291 490 Planarity : 0.011 0.083 601 Dihedral : 14.445 89.737 1221 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -2.94 (0.36), residues: 419 helix: -4.41 (0.43), residues: 30 sheet: -0.69 (0.47), residues: 125 loop : -2.41 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP H 117 HIS 0.002 0.001 HIS H 106 PHE 0.035 0.004 PHE E 377 TYR 0.050 0.003 TYR E 453 ARG 0.023 0.002 ARG H 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 386 LYS cc_start: 0.8113 (pttt) cc_final: 0.7753 (tptm) REVERT: L 27 GLN cc_start: 0.7584 (tm-30) cc_final: 0.7296 (tm-30) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1878 time to fit residues: 19.6934 Evaluate side-chains 76 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 10 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.0270 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.2438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 90 GLN L 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3404 Z= 0.205 Angle : 0.628 7.112 4620 Z= 0.326 Chirality : 0.045 0.176 490 Planarity : 0.006 0.062 601 Dihedral : 5.678 32.933 470 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 1.94 % Allowed : 13.89 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.37), residues: 419 helix: -3.78 (0.63), residues: 30 sheet: -0.44 (0.48), residues: 120 loop : -2.28 (0.33), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 36 HIS 0.003 0.001 HIS E 519 PHE 0.017 0.002 PHE E 456 TYR 0.015 0.002 TYR E 501 ARG 0.005 0.001 ARG H 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 84 average time/residue: 0.1876 time to fit residues: 18.5692 Evaluate side-chains 85 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 53 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN L 55 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3404 Z= 0.287 Angle : 0.655 8.087 4620 Z= 0.339 Chirality : 0.046 0.206 490 Planarity : 0.006 0.052 601 Dihedral : 5.693 34.168 470 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 2.22 % Allowed : 19.44 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.38), residues: 419 helix: -2.66 (1.00), residues: 24 sheet: -0.52 (0.49), residues: 117 loop : -2.07 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 36 HIS 0.001 0.000 HIS H 106 PHE 0.021 0.002 PHE H 64 TYR 0.018 0.002 TYR L 49 ARG 0.007 0.001 ARG L 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 498 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.7649 (mtm-85) outliers start: 8 outliers final: 7 residues processed: 87 average time/residue: 0.2105 time to fit residues: 21.5742 Evaluate side-chains 76 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.0670 chunk 33 optimal weight: 0.0050 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 0.7980 overall best weight: 0.2132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3404 Z= 0.184 Angle : 0.598 7.090 4620 Z= 0.305 Chirality : 0.044 0.172 490 Planarity : 0.005 0.049 601 Dihedral : 5.267 31.608 470 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.50 % Allowed : 20.28 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.39), residues: 419 helix: -2.11 (1.09), residues: 24 sheet: -0.24 (0.49), residues: 117 loop : -1.92 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 36 HIS 0.001 0.000 HIS E 519 PHE 0.017 0.001 PHE E 456 TYR 0.011 0.001 TYR L 49 ARG 0.004 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 378 LYS cc_start: 0.7697 (tptp) cc_final: 0.7455 (tptm) REVERT: E 467 ASP cc_start: 0.7574 (p0) cc_final: 0.7286 (p0) REVERT: E 498 ARG cc_start: 0.7906 (mtm-85) cc_final: 0.7583 (mtm-85) REVERT: H 110 TYR cc_start: 0.7569 (t80) cc_final: 0.7327 (t80) REVERT: L 27 GLN cc_start: 0.7537 (tm-30) cc_final: 0.6615 (tm-30) outliers start: 9 outliers final: 5 residues processed: 77 average time/residue: 0.2176 time to fit residues: 19.4317 Evaluate side-chains 78 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.0060 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 0.2980 chunk 0 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN L 55 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3404 Z= 0.272 Angle : 0.633 8.040 4620 Z= 0.327 Chirality : 0.046 0.202 490 Planarity : 0.005 0.050 601 Dihedral : 5.487 32.942 470 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 3.33 % Allowed : 20.00 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.39), residues: 419 helix: -1.88 (1.15), residues: 24 sheet: -0.44 (0.49), residues: 118 loop : -1.81 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP H 36 HIS 0.001 0.000 HIS E 519 PHE 0.021 0.002 PHE H 64 TYR 0.017 0.002 TYR L 49 ARG 0.005 0.001 ARG E 493 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 467 ASP cc_start: 0.7724 (p0) cc_final: 0.7469 (p0) REVERT: L 27 GLN cc_start: 0.7641 (tm-30) cc_final: 0.6737 (tm-30) outliers start: 12 outliers final: 8 residues processed: 83 average time/residue: 0.2070 time to fit residues: 19.9411 Evaluate side-chains 81 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.0570 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.0570 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN L 55 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3404 Z= 0.251 Angle : 0.635 7.874 4620 Z= 0.327 Chirality : 0.045 0.196 490 Planarity : 0.005 0.050 601 Dihedral : 5.459 32.883 470 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 4.44 % Allowed : 21.11 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.39), residues: 419 helix: -1.94 (1.11), residues: 24 sheet: -0.42 (0.49), residues: 119 loop : -1.80 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 36 HIS 0.001 0.000 HIS E 519 PHE 0.024 0.002 PHE E 456 TYR 0.014 0.002 TYR L 49 ARG 0.006 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 467 ASP cc_start: 0.7691 (p0) cc_final: 0.7425 (p0) REVERT: L 27 GLN cc_start: 0.7618 (tm-30) cc_final: 0.6707 (tm-30) outliers start: 16 outliers final: 9 residues processed: 84 average time/residue: 0.2014 time to fit residues: 19.6685 Evaluate side-chains 82 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 18 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 7 optimal weight: 0.0770 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN E 477 ASN L 55 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3404 Z= 0.231 Angle : 0.621 7.761 4620 Z= 0.321 Chirality : 0.045 0.189 490 Planarity : 0.005 0.052 601 Dihedral : 5.401 33.019 470 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 4.17 % Allowed : 21.39 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.39), residues: 419 helix: -1.98 (1.09), residues: 24 sheet: -0.45 (0.49), residues: 118 loop : -1.74 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 117 HIS 0.001 0.000 HIS E 519 PHE 0.017 0.002 PHE H 64 TYR 0.013 0.001 TYR L 49 ARG 0.006 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 414 GLN cc_start: 0.6845 (mp10) cc_final: 0.6571 (mp10) REVERT: L 27 GLN cc_start: 0.7556 (tm-30) cc_final: 0.6696 (tm-30) REVERT: L 42 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7796 (mttt) outliers start: 15 outliers final: 12 residues processed: 86 average time/residue: 0.1961 time to fit residues: 19.8169 Evaluate side-chains 83 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 480 CYS Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN L 55 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 3404 Z= 0.400 Angle : 0.731 9.594 4620 Z= 0.381 Chirality : 0.049 0.260 490 Planarity : 0.006 0.052 601 Dihedral : 6.104 38.310 470 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 4.44 % Allowed : 22.78 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.37), residues: 419 helix: -2.94 (1.03), residues: 18 sheet: -0.82 (0.48), residues: 119 loop : -2.03 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP H 117 HIS 0.002 0.001 HIS H 106 PHE 0.029 0.003 PHE H 64 TYR 0.020 0.002 TYR L 49 ARG 0.006 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 378 LYS cc_start: 0.8398 (tptp) cc_final: 0.8012 (tppt) REVERT: E 467 ASP cc_start: 0.7838 (p0) cc_final: 0.7547 (p0) REVERT: L 27 GLN cc_start: 0.7673 (tm-30) cc_final: 0.6803 (tm-30) REVERT: L 90 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8636 (tm-30) outliers start: 16 outliers final: 9 residues processed: 94 average time/residue: 0.1892 time to fit residues: 20.8753 Evaluate side-chains 89 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 480 CYS Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 71.0489 > 50: distance: 31 - 37: 29.610 distance: 37 - 38: 53.323 distance: 38 - 39: 40.237 distance: 38 - 41: 17.703 distance: 39 - 40: 34.677 distance: 39 - 48: 42.000 distance: 41 - 42: 4.420 distance: 42 - 43: 20.827 distance: 43 - 44: 36.149 distance: 44 - 45: 27.632 distance: 45 - 46: 12.907 distance: 45 - 47: 7.060 distance: 48 - 49: 23.056 distance: 49 - 50: 49.057 distance: 49 - 52: 15.084 distance: 50 - 51: 8.251 distance: 50 - 56: 49.087 distance: 52 - 53: 32.944 distance: 53 - 54: 25.366 distance: 53 - 55: 25.548 distance: 56 - 57: 41.602 distance: 57 - 58: 52.528 distance: 57 - 60: 17.269 distance: 58 - 59: 29.970 distance: 58 - 64: 43.741 distance: 60 - 61: 42.501 distance: 61 - 62: 34.355 distance: 61 - 63: 38.394 distance: 64 - 65: 28.929 distance: 65 - 66: 49.891 distance: 65 - 68: 12.959 distance: 66 - 67: 45.193 distance: 66 - 72: 23.131 distance: 68 - 69: 39.978 distance: 69 - 70: 26.932 distance: 69 - 71: 26.401 distance: 72 - 73: 22.609 distance: 72 - 271: 15.180 distance: 73 - 74: 60.640 distance: 74 - 75: 28.651 distance: 74 - 76: 38.083 distance: 75 - 268: 26.646 distance: 76 - 77: 19.185 distance: 77 - 78: 44.993 distance: 77 - 80: 16.280 distance: 78 - 79: 7.571 distance: 78 - 90: 34.557 distance: 79 - 170: 27.225 distance: 80 - 81: 29.747 distance: 81 - 82: 13.942 distance: 81 - 83: 15.284 distance: 82 - 84: 17.510 distance: 83 - 85: 29.348 distance: 83 - 86: 16.098 distance: 84 - 85: 19.895 distance: 85 - 87: 29.335 distance: 86 - 88: 23.349 distance: 87 - 89: 12.682 distance: 88 - 89: 25.969 distance: 90 - 91: 13.938 distance: 90 - 256: 17.037 distance: 91 - 92: 50.904 distance: 91 - 94: 22.080 distance: 92 - 102: 43.721 distance: 93 - 253: 34.355 distance: 94 - 95: 52.050 distance: 95 - 96: 16.207 distance: 95 - 97: 17.967 distance: 96 - 98: 30.271 distance: 97 - 99: 18.808 distance: 98 - 100: 21.743 distance: 99 - 100: 40.242 distance: 100 - 101: 7.471 distance: 102 - 103: 30.896 distance: 102 - 160: 25.967 distance: 103 - 104: 45.749 distance: 103 - 106: 24.286 distance: 104 - 111: 29.669 distance: 105 - 157: 33.559 distance: 106 - 107: 36.347 distance: 107 - 108: 24.103 distance: 108 - 109: 15.459 distance: 108 - 110: 18.538 distance: 111 - 112: 22.312 distance: 111 - 239: 20.109 distance: 112 - 113: 60.264 distance: 112 - 115: 37.025 distance: 113 - 114: 48.730 distance: 113 - 120: 32.940 distance: 114 - 236: 32.568 distance: 115 - 116: 33.821 distance: 116 - 117: 20.913 distance: 117 - 118: 17.641 distance: 117 - 119: 8.384 distance: 120 - 121: 4.113 distance: 121 - 122: 23.979 distance: 121 - 124: 39.265 distance: 122 - 123: 20.315 distance: 122 - 129: 28.832 distance: 124 - 125: 63.112 distance: 125 - 126: 50.118 distance: 126 - 127: 41.607 distance: 127 - 128: 63.606