Starting phenix.real_space_refine on Tue Feb 13 09:31:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezv_31391/02_2024/7ezv_31391.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezv_31391/02_2024/7ezv_31391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezv_31391/02_2024/7ezv_31391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezv_31391/02_2024/7ezv_31391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezv_31391/02_2024/7ezv_31391.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezv_31391/02_2024/7ezv_31391.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.049 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 22 5.16 5 C 3131 2.51 5 N 835 2.21 5 O 949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "H GLU 26": "OE1" <-> "OE2" Residue "H ASP 55": "OD1" <-> "OD2" Residue "H ASP 57": "OD1" <-> "OD2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 66": "OE1" <-> "OE2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4937 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "H" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 912 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "M" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 927 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "N" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Time building chain proxies: 3.28, per 1000 atoms: 0.66 Number of scatterers: 4937 At special positions: 0 Unit cell: (99.36, 90.72, 98.28, 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 22 16.00 O 949 8.00 N 835 7.00 C 3131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 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 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 101 " - pdb=" SG CYS M 106 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 89 " 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: 1.83 Conformation dependent library (CDL) restraints added in 1.3 seconds 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 13 sheets defined 9.3% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.025A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.752A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.698A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 31 Processing helix chain 'M' and resid 73 through 76 Processing helix chain 'M' and resid 101 through 105 removed outlier: 3.778A pdb=" N GLY M 104 " --> pdb=" O CYS M 101 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR M 105 " --> pdb=" O SER M 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 101 through 105' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.501A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA5, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 44 through 48 removed outlier: 6.378A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'M' and resid 57 through 60 removed outlier: 6.725A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TRP M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 57 through 60 removed outlier: 6.725A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TRP M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.029A pdb=" N LEU N 11 " --> pdb=" O GLU N 106 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR N 103 " --> pdb=" O TYR N 87 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) 175 hydrogen bonds defined for protein. 411 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: 1.30 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 867 1.32 - 1.45: 1451 1.45 - 1.57: 2715 1.57 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 5060 Sorted by residual: bond pdb=" CA ALA A 475 " pdb=" CB ALA A 475 " ideal model delta sigma weight residual 1.532 1.490 0.042 1.53e-02 4.27e+03 7.58e+00 bond pdb=" N THR A 478 " pdb=" CA THR A 478 " ideal model delta sigma weight residual 1.453 1.483 -0.030 1.16e-02 7.43e+03 6.64e+00 bond pdb=" C PRO A 479 " pdb=" O PRO A 479 " ideal model delta sigma weight residual 1.233 1.205 0.028 1.16e-02 7.43e+03 5.93e+00 bond pdb=" CA SER A 477 " pdb=" CB SER A 477 " ideal model delta sigma weight residual 1.530 1.491 0.038 1.63e-02 3.76e+03 5.56e+00 bond pdb=" N ASN A 481 " pdb=" CA ASN A 481 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.39e-02 5.18e+03 3.97e+00 ... (remaining 5055 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.60: 135 106.60 - 113.45: 2649 113.45 - 120.30: 1774 120.30 - 127.14: 2260 127.14 - 133.99: 55 Bond angle restraints: 6873 Sorted by residual: angle pdb=" C PRO A 479 " pdb=" CA PRO A 479 " pdb=" CB PRO A 479 " ideal model delta sigma weight residual 111.46 105.43 6.03 1.29e+00 6.01e-01 2.18e+01 angle pdb=" C GLY A 482 " pdb=" N VAL A 483 " pdb=" CA VAL A 483 " ideal model delta sigma weight residual 123.13 118.95 4.18 1.34e+00 5.57e-01 9.74e+00 angle pdb=" CA SER A 477 " pdb=" C SER A 477 " pdb=" O SER A 477 " ideal model delta sigma weight residual 120.55 117.27 3.28 1.07e+00 8.73e-01 9.39e+00 angle pdb=" C ALA L 51 " pdb=" N SER L 52 " pdb=" CA SER L 52 " ideal model delta sigma weight residual 121.54 127.33 -5.79 1.91e+00 2.74e-01 9.20e+00 angle pdb=" N ALA A 475 " pdb=" CA ALA A 475 " pdb=" C ALA A 475 " ideal model delta sigma weight residual 113.41 109.71 3.70 1.22e+00 6.72e-01 9.18e+00 ... (remaining 6868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 2692 17.47 - 34.93: 233 34.93 - 52.40: 45 52.40 - 69.87: 7 69.87 - 87.33: 3 Dihedral angle restraints: 2980 sinusoidal: 1160 harmonic: 1820 Sorted by residual: dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 89 " pdb=" CB CYS N 89 " ideal model delta sinusoidal sigma weight residual 93.00 156.07 -63.07 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CA ALA L 94 " pdb=" C ALA L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual -180.00 -143.91 -36.09 0 5.00e+00 4.00e-02 5.21e+01 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 93.00 147.80 -54.80 1 1.00e+01 1.00e-02 4.07e+01 ... (remaining 2977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 521 0.040 - 0.081: 144 0.081 - 0.121: 56 0.121 - 0.162: 14 0.162 - 0.202: 3 Chirality restraints: 738 Sorted by residual: chirality pdb=" CA PRO L 95 " pdb=" N PRO L 95 " pdb=" C PRO L 95 " pdb=" CB PRO L 95 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE M 51 " pdb=" N ILE M 51 " pdb=" C ILE M 51 " pdb=" CB ILE M 51 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CA CYS A 480 " pdb=" N CYS A 480 " pdb=" C CYS A 480 " pdb=" CB CYS A 480 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 735 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 94 " -0.089 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO L 95 " 0.235 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 65 " 0.120 9.50e-02 1.11e+02 5.45e-02 2.48e+00 pdb=" NE ARG L 65 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG L 65 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG L 65 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG L 65 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU N 80 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO N 81 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO N 81 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO N 81 " -0.022 5.00e-02 4.00e+02 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 56 2.61 - 3.18: 4302 3.18 - 3.75: 7412 3.75 - 4.33: 10832 4.33 - 4.90: 18369 Nonbonded interactions: 40971 Sorted by model distance: nonbonded pdb=" OG1 THR M 28 " pdb=" O CYS M 101 " model vdw 2.034 2.440 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.173 2.440 nonbonded pdb=" NH2 ARG A 346 " pdb=" OD2 ASP H 54 " model vdw 2.248 2.520 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.252 2.440 nonbonded pdb=" OD2 ASP M 73 " pdb=" OG1 THR M 76 " model vdw 2.290 2.440 ... (remaining 40966 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 individual isotropic 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: 2.360 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: 9.560 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 18.510 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 0.049 5060 Z= 0.326 Angle : 0.712 9.008 6873 Z= 0.394 Chirality : 0.047 0.202 738 Planarity : 0.007 0.136 883 Dihedral : 13.537 87.335 1804 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.36 % Favored : 91.32 % Rotamer: Outliers : 0.75 % Allowed : 0.75 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -0.96 (0.33), residues: 622 helix: -3.09 (0.74), residues: 27 sheet: -0.21 (0.33), residues: 253 loop : -0.69 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 36 HIS 0.006 0.004 HIS M 100 PHE 0.018 0.002 PHE H 24 TYR 0.015 0.002 TYR L 91 ARG 0.014 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: L 90 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8752 (pp30) REVERT: N 101 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7772 (pp30) outliers start: 4 outliers final: 0 residues processed: 104 average time/residue: 0.2416 time to fit residues: 30.0152 Evaluate side-chains 88 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain N residue 101 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 5.9990 chunk 46 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN L 90 GLN M 39 GLN M 100 HIS N 39 GLN N 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5060 Z= 0.210 Angle : 0.600 7.435 6873 Z= 0.314 Chirality : 0.045 0.154 738 Planarity : 0.004 0.040 883 Dihedral : 5.876 41.047 709 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.72 % Favored : 92.12 % Rotamer: Outliers : 2.05 % Allowed : 8.58 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -0.95 (0.34), residues: 622 helix: -2.83 (0.87), residues: 27 sheet: -0.15 (0.33), residues: 249 loop : -0.75 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 36 HIS 0.003 0.002 HIS M 100 PHE 0.013 0.001 PHE H 24 TYR 0.013 0.001 TYR M 107 ARG 0.007 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8502 (mtm110) cc_final: 0.8287 (ptp-110) REVERT: M 27 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7475 (m-80) REVERT: M 73 ASP cc_start: 0.7334 (t0) cc_final: 0.6968 (t0) REVERT: M 80 TYR cc_start: 0.8196 (m-80) cc_final: 0.7890 (m-10) outliers start: 11 outliers final: 4 residues processed: 103 average time/residue: 0.2270 time to fit residues: 28.3540 Evaluate side-chains 85 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN M 39 GLN ** N 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5060 Z= 0.228 Angle : 0.582 6.305 6873 Z= 0.305 Chirality : 0.045 0.201 738 Planarity : 0.004 0.039 883 Dihedral : 5.357 35.746 703 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.04 % Favored : 91.80 % Rotamer: Outliers : 1.87 % Allowed : 10.63 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -0.94 (0.34), residues: 622 helix: -2.99 (0.81), residues: 27 sheet: -0.12 (0.33), residues: 250 loop : -0.76 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 36 HIS 0.000 0.000 HIS M 100 PHE 0.012 0.001 PHE H 24 TYR 0.014 0.001 TYR M 107 ARG 0.008 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8550 (ptmm) REVERT: A 406 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8235 (mt-10) REVERT: A 408 ARG cc_start: 0.8530 (mtm110) cc_final: 0.8234 (ptp-110) REVERT: M 73 ASP cc_start: 0.7339 (t0) cc_final: 0.7006 (t0) REVERT: M 80 TYR cc_start: 0.8195 (m-80) cc_final: 0.7875 (m-10) REVERT: N 104 LYS cc_start: 0.7435 (tmmt) cc_final: 0.7074 (ttpp) outliers start: 10 outliers final: 3 residues processed: 93 average time/residue: 0.2713 time to fit residues: 30.3765 Evaluate side-chains 87 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** N 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5060 Z= 0.328 Angle : 0.631 7.633 6873 Z= 0.332 Chirality : 0.046 0.172 738 Planarity : 0.004 0.040 883 Dihedral : 5.513 24.875 703 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.00 % Favored : 90.84 % Rotamer: Outliers : 3.92 % Allowed : 10.63 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.34), residues: 622 helix: -2.90 (0.82), residues: 27 sheet: -0.25 (0.33), residues: 262 loop : -0.74 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 36 HIS 0.001 0.001 HIS M 100 PHE 0.011 0.002 PHE N 99 TYR 0.018 0.002 TYR L 91 ARG 0.010 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8229 (ptp-110) REVERT: M 27 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7400 (m-80) REVERT: M 73 ASP cc_start: 0.7564 (t0) cc_final: 0.7325 (t0) REVERT: M 80 TYR cc_start: 0.8261 (m-80) cc_final: 0.7969 (m-10) REVERT: N 104 LYS cc_start: 0.7700 (tmmt) cc_final: 0.7389 (ttpp) outliers start: 21 outliers final: 12 residues processed: 93 average time/residue: 0.2507 time to fit residues: 27.9428 Evaluate side-chains 95 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 79 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 40 optimal weight: 0.0060 chunk 30 optimal weight: 4.9990 chunk 52 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN M 39 GLN N 39 GLN ** N 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5060 Z= 0.206 Angle : 0.577 6.804 6873 Z= 0.304 Chirality : 0.045 0.171 738 Planarity : 0.004 0.043 883 Dihedral : 5.206 24.966 703 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.23 % Favored : 92.60 % Rotamer: Outliers : 3.54 % Allowed : 12.50 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.34), residues: 622 helix: -2.80 (0.85), residues: 26 sheet: -0.22 (0.33), residues: 262 loop : -0.63 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 83 HIS 0.000 0.000 HIS M 100 PHE 0.011 0.001 PHE H 24 TYR 0.014 0.001 TYR L 91 ARG 0.010 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8584 (ptmm) REVERT: A 406 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8191 (mt-10) REVERT: A 408 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8187 (ptp-110) REVERT: A 420 ASP cc_start: 0.8318 (m-30) cc_final: 0.8082 (m-30) REVERT: L 27 GLN cc_start: 0.7815 (mp10) cc_final: 0.7426 (mp10) REVERT: M 19 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8334 (mmm160) REVERT: M 27 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7332 (m-80) REVERT: N 104 LYS cc_start: 0.7591 (tmmt) cc_final: 0.7290 (ttpp) outliers start: 19 outliers final: 11 residues processed: 95 average time/residue: 0.2498 time to fit residues: 28.4510 Evaluate side-chains 97 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 79 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 0.2980 chunk 14 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 56 optimal weight: 0.1980 chunk 6 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN L 37 GLN M 39 GLN ** N 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5060 Z= 0.184 Angle : 0.576 6.440 6873 Z= 0.302 Chirality : 0.044 0.154 738 Planarity : 0.004 0.045 883 Dihedral : 5.021 24.894 703 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.88 % Favored : 91.96 % Rotamer: Outliers : 3.17 % Allowed : 13.99 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.34), residues: 622 helix: -2.72 (0.87), residues: 26 sheet: -0.05 (0.33), residues: 256 loop : -0.63 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 83 HIS 0.001 0.001 HIS M 100 PHE 0.010 0.001 PHE H 24 TYR 0.015 0.001 TYR M 107 ARG 0.011 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8218 (mt-10) REVERT: A 408 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8160 (ptp-110) REVERT: A 420 ASP cc_start: 0.8303 (m-30) cc_final: 0.8056 (m-30) REVERT: L 27 GLN cc_start: 0.7824 (mp10) cc_final: 0.7485 (mp10) REVERT: M 27 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7215 (m-80) REVERT: M 80 TYR cc_start: 0.8008 (m-80) cc_final: 0.7766 (m-10) REVERT: N 104 LYS cc_start: 0.7613 (tmmt) cc_final: 0.7318 (ttpp) outliers start: 17 outliers final: 11 residues processed: 96 average time/residue: 0.2490 time to fit residues: 28.6133 Evaluate side-chains 97 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 79 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** N 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5060 Z= 0.352 Angle : 0.651 7.478 6873 Z= 0.343 Chirality : 0.046 0.148 738 Planarity : 0.005 0.047 883 Dihedral : 5.407 24.515 703 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.16 % Favored : 90.68 % Rotamer: Outliers : 3.54 % Allowed : 14.93 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.34), residues: 622 helix: -2.78 (0.83), residues: 27 sheet: -0.22 (0.33), residues: 260 loop : -0.65 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 36 HIS 0.001 0.000 HIS M 100 PHE 0.011 0.002 PHE M 27 TYR 0.021 0.002 TYR L 91 ARG 0.012 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8213 (mt-10) REVERT: A 408 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8256 (ptp-110) REVERT: A 420 ASP cc_start: 0.8326 (m-30) cc_final: 0.8117 (m-30) REVERT: L 27 GLN cc_start: 0.7987 (mp10) cc_final: 0.7595 (mp10) REVERT: M 27 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7372 (m-80) REVERT: N 104 LYS cc_start: 0.7844 (tmmt) cc_final: 0.7557 (tmmt) outliers start: 19 outliers final: 12 residues processed: 91 average time/residue: 0.2638 time to fit residues: 28.6171 Evaluate side-chains 95 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 79 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 0.0020 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 overall best weight: 0.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 39 GLN N 39 GLN ** N 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5060 Z= 0.167 Angle : 0.576 5.929 6873 Z= 0.303 Chirality : 0.044 0.146 738 Planarity : 0.005 0.049 883 Dihedral : 4.930 25.053 703 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.27 % Favored : 93.57 % Rotamer: Outliers : 2.99 % Allowed : 16.42 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.35), residues: 622 helix: -2.21 (1.16), residues: 18 sheet: -0.17 (0.34), residues: 260 loop : -0.44 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 83 HIS 0.001 0.000 HIS M 100 PHE 0.011 0.001 PHE H 24 TYR 0.013 0.001 TYR M 107 ARG 0.013 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8244 (mt-10) REVERT: A 408 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8140 (ptp-110) REVERT: A 420 ASP cc_start: 0.8299 (m-30) cc_final: 0.8062 (m-30) REVERT: A 468 ILE cc_start: 0.9427 (pt) cc_final: 0.9127 (mt) REVERT: L 27 GLN cc_start: 0.7859 (mp10) cc_final: 0.7565 (mp10) REVERT: M 27 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.7153 (m-80) REVERT: N 104 LYS cc_start: 0.7557 (tmmt) cc_final: 0.7276 (tmmt) outliers start: 16 outliers final: 12 residues processed: 94 average time/residue: 0.2504 time to fit residues: 28.1497 Evaluate side-chains 94 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 3 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN ** N 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5060 Z= 0.325 Angle : 0.648 6.536 6873 Z= 0.341 Chirality : 0.045 0.149 738 Planarity : 0.005 0.053 883 Dihedral : 5.274 25.308 703 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.52 % Favored : 91.32 % Rotamer: Outliers : 3.54 % Allowed : 16.23 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.34), residues: 622 helix: -2.90 (0.82), residues: 27 sheet: -0.19 (0.34), residues: 255 loop : -0.50 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 36 HIS 0.000 0.000 HIS M 100 PHE 0.009 0.002 PHE M 27 TYR 0.026 0.002 TYR M 80 ARG 0.014 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8242 (ptp-110) REVERT: A 420 ASP cc_start: 0.8289 (m-30) cc_final: 0.8058 (m-30) REVERT: L 27 GLN cc_start: 0.7967 (mp10) cc_final: 0.7614 (mp10) REVERT: M 3 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8311 (pp30) REVERT: M 27 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7237 (m-80) REVERT: N 104 LYS cc_start: 0.7825 (tmmt) cc_final: 0.7546 (tmmt) outliers start: 19 outliers final: 15 residues processed: 92 average time/residue: 0.2479 time to fit residues: 27.5105 Evaluate side-chains 97 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.0570 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 39 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5060 Z= 0.181 Angle : 0.614 6.615 6873 Z= 0.325 Chirality : 0.045 0.163 738 Planarity : 0.005 0.059 883 Dihedral : 4.982 26.376 703 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.75 % Favored : 93.09 % Rotamer: Outliers : 2.80 % Allowed : 17.35 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.35), residues: 622 helix: -2.72 (1.04), residues: 19 sheet: -0.20 (0.33), residues: 268 loop : -0.42 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 83 HIS 0.000 0.000 HIS M 100 PHE 0.011 0.001 PHE H 24 TYR 0.018 0.001 TYR M 107 ARG 0.014 0.001 ARG L 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8175 (mt-10) REVERT: A 408 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8229 (ptp-110) REVERT: A 420 ASP cc_start: 0.8270 (m-30) cc_final: 0.8019 (m-30) REVERT: A 468 ILE cc_start: 0.9425 (pt) cc_final: 0.9130 (mt) REVERT: L 27 GLN cc_start: 0.7865 (mp10) cc_final: 0.7589 (mp10) REVERT: M 27 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: N 104 LYS cc_start: 0.7628 (tmmt) cc_final: 0.7347 (tmmt) outliers start: 15 outliers final: 12 residues processed: 91 average time/residue: 0.2480 time to fit residues: 27.2136 Evaluate side-chains 95 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 3 GLN M 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.071241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.059813 restraints weight = 14080.801| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.69 r_work: 0.2920 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5060 Z= 0.227 Angle : 0.611 5.909 6873 Z= 0.322 Chirality : 0.044 0.148 738 Planarity : 0.005 0.058 883 Dihedral : 4.974 25.686 703 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.40 % Favored : 92.44 % Rotamer: Outliers : 2.99 % Allowed : 16.60 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.34), residues: 622 helix: -3.04 (0.81), residues: 26 sheet: -0.24 (0.34), residues: 265 loop : -0.39 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 36 HIS 0.000 0.000 HIS M 100 PHE 0.010 0.001 PHE H 24 TYR 0.017 0.001 TYR M 107 ARG 0.014 0.001 ARG L 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1619.00 seconds wall clock time: 29 minutes 53.84 seconds (1793.84 seconds total)