Starting phenix.real_space_refine on Thu Jul 18 22:03:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4c_18885/07_2024/8r4c_18885.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4c_18885/07_2024/8r4c_18885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4c_18885/07_2024/8r4c_18885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4c_18885/07_2024/8r4c_18885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4c_18885/07_2024/8r4c_18885.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r4c_18885/07_2024/8r4c_18885.cif" } resolution = 3.55 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= 0.140 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 9 5.16 5 C 2541 2.51 5 N 669 2.21 5 O 808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4027 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 843 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 112} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3184 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 22, 'TRANS': 414} Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 13, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 95 Time building chain proxies: 2.76, per 1000 atoms: 0.69 Number of scatterers: 4027 At special positions: 0 Unit cell: (54.6476, 73.3429, 104.981, 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 9 16.00 O 808 8.00 N 669 7.00 C 2541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " 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: 1.40 Conformation dependent library (CDL) restraints added in 749.4 milliseconds 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1054 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 6 sheets defined 19.7% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.848A pdb=" N THR C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 51 through 62 removed outlier: 3.736A pdb=" N ILE A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Proline residue: A 58 - end of helix removed outlier: 3.617A pdb=" N LEU A 62 " --> pdb=" O PRO A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 4.089A pdb=" N SER A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 removed outlier: 3.522A pdb=" N SER A 149 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 172 Processing helix chain 'A' and resid 211 through 216 removed outlier: 4.089A pdb=" N GLU A 214 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.904A pdb=" N SER A 237 " --> pdb=" O PRO A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 260 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.740A pdb=" N LEU A 345 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 419 through 426 removed outlier: 3.790A pdb=" N GLY A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 439 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.184A pdb=" N GLY C 10 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL C 33 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.184A pdb=" N GLY C 10 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLY C 99 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASN C 107 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE C 101 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N TYR C 105 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 19 through 20 removed outlier: 6.297A pdb=" N GLU A 19 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 30 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 41 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU A 222 " --> pdb=" O GLN A 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 267 removed outlier: 6.842A pdb=" N LEU A 310 " --> pdb=" O TRP A 333 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 376 through 377 removed outlier: 6.411A pdb=" N GLU A 396 " --> pdb=" O ILE A 408 " (cutoff:3.500A) 111 hydrogen bonds defined for protein. 240 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: 1.09 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1323 1.34 - 1.46: 526 1.46 - 1.57: 2222 1.57 - 1.69: 0 1.69 - 1.81: 15 Bond restraints: 4086 Sorted by residual: bond pdb=" N PRO A 414 " pdb=" CA PRO A 414 " ideal model delta sigma weight residual 1.469 1.485 -0.016 1.28e-02 6.10e+03 1.57e+00 bond pdb=" CB ILE A 144 " pdb=" CG1 ILE A 144 " ideal model delta sigma weight residual 1.530 1.554 -0.024 2.00e-02 2.50e+03 1.42e+00 bond pdb=" CA ILE A 144 " pdb=" CB ILE A 144 " ideal model delta sigma weight residual 1.540 1.556 -0.016 1.36e-02 5.41e+03 1.40e+00 bond pdb=" CB VAL C 48 " pdb=" CG2 VAL C 48 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.92e-01 bond pdb=" CB CYS C 95 " pdb=" SG CYS C 95 " ideal model delta sigma weight residual 1.808 1.780 0.028 3.30e-02 9.18e+02 7.39e-01 ... (remaining 4081 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.95: 120 106.95 - 113.72: 2379 113.72 - 120.48: 1433 120.48 - 127.25: 1616 127.25 - 134.01: 39 Bond angle restraints: 5587 Sorted by residual: angle pdb=" N ILE A 166 " pdb=" CA ILE A 166 " pdb=" C ILE A 166 " ideal model delta sigma weight residual 113.20 109.27 3.93 9.60e-01 1.09e+00 1.68e+01 angle pdb=" CB ILE A 144 " pdb=" CG1 ILE A 144 " pdb=" CD1 ILE A 144 " ideal model delta sigma weight residual 113.80 121.51 -7.71 2.10e+00 2.27e-01 1.35e+01 angle pdb=" CA ILE A 144 " pdb=" CB ILE A 144 " pdb=" CG1 ILE A 144 " ideal model delta sigma weight residual 110.40 116.38 -5.98 1.70e+00 3.46e-01 1.24e+01 angle pdb=" CA GLN A 12 " pdb=" CB GLN A 12 " pdb=" CG GLN A 12 " ideal model delta sigma weight residual 114.10 120.42 -6.32 2.00e+00 2.50e-01 9.99e+00 angle pdb=" N ALA C 91 " pdb=" CA ALA C 91 " pdb=" C ALA C 91 " ideal model delta sigma weight residual 108.34 112.10 -3.76 1.31e+00 5.83e-01 8.24e+00 ... (remaining 5582 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 2071 16.71 - 33.43: 319 33.43 - 50.14: 88 50.14 - 66.85: 16 66.85 - 83.56: 7 Dihedral angle restraints: 2501 sinusoidal: 886 harmonic: 1615 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sinusoidal sigma weight residual 93.00 167.85 -74.85 1 1.00e+01 1.00e-02 7.09e+01 dihedral pdb=" CA LYS A 173 " pdb=" C LYS A 173 " pdb=" N SER A 174 " pdb=" CA SER A 174 " ideal model delta harmonic sigma weight residual 180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA SER A 203 " pdb=" C SER A 203 " pdb=" N SER A 204 " pdb=" CA SER A 204 " ideal model delta harmonic sigma weight residual 180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 2498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 417 0.033 - 0.066: 196 0.066 - 0.099: 61 0.099 - 0.131: 25 0.131 - 0.164: 2 Chirality restraints: 701 Sorted by residual: chirality pdb=" CA ILE A 408 " pdb=" N ILE A 408 " pdb=" C ILE A 408 " pdb=" CB ILE A 408 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CB ILE A 144 " pdb=" CA ILE A 144 " pdb=" CG1 ILE A 144 " pdb=" CG2 ILE A 144 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE A 210 " pdb=" N ILE A 210 " pdb=" C ILE A 210 " pdb=" CB ILE A 210 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 698 not shown) Planarity restraints: 715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 413 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO A 414 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 414 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 414 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 189 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO A 190 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 190 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 190 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 233 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 234 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " -0.023 5.00e-02 4.00e+02 ... (remaining 712 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 404 2.75 - 3.28: 3926 3.28 - 3.82: 6653 3.82 - 4.36: 8050 4.36 - 4.90: 13681 Nonbonded interactions: 32714 Sorted by model distance: nonbonded pdb=" OD1 ASN C 32 " pdb=" OH TYR A 45 " model vdw 2.207 2.440 nonbonded pdb=" O SER A 417 " pdb=" OH TYR A 433 " model vdw 2.275 2.440 nonbonded pdb=" OG1 THR A 154 " pdb=" OE1 GLU A 155 " model vdw 2.283 2.440 nonbonded pdb=" O SER A 352 " pdb=" OG1 THR A 374 " model vdw 2.286 2.440 nonbonded pdb=" O SER A 286 " pdb=" OG1 THR A 308 " model vdw 2.301 2.440 ... (remaining 32709 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: 0.000 Normalize map: mean=0, sd=1: 0.210 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.180 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 : 0.004 0.031 4086 Z= 0.231 Angle : 0.718 7.710 5587 Z= 0.378 Chirality : 0.044 0.164 701 Planarity : 0.005 0.047 715 Dihedral : 17.999 83.565 1444 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 1.16 % Allowed : 36.28 % Favored : 62.56 % 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: -2.95 (0.34), residues: 549 helix: -1.38 (0.57), residues: 95 sheet: -1.81 (0.43), residues: 135 loop : -2.26 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 36 HIS 0.001 0.000 HIS C 109 PHE 0.014 0.002 PHE A 410 TYR 0.011 0.001 TYR C 37 ARG 0.007 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 0.459 Fit side-chains REVERT: A 214 GLU cc_start: 0.6355 (mp0) cc_final: 0.6038 (mp0) REVERT: A 376 PHE cc_start: 0.8570 (t80) cc_final: 0.8106 (t80) outliers start: 5 outliers final: 3 residues processed: 129 average time/residue: 0.1680 time to fit residues: 26.5286 Evaluate side-chains 129 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain A residue 409 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.0516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4086 Z= 0.256 Angle : 0.663 7.225 5587 Z= 0.335 Chirality : 0.043 0.180 701 Planarity : 0.005 0.043 715 Dihedral : 5.624 38.460 583 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 7.91 % Allowed : 29.77 % Favored : 62.33 % 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: -2.91 (0.34), residues: 549 helix: -1.21 (0.56), residues: 102 sheet: -1.75 (0.43), residues: 139 loop : -2.31 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 36 HIS 0.001 0.001 HIS C 109 PHE 0.015 0.002 PHE A 410 TYR 0.008 0.001 TYR C 94 ARG 0.006 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 0.472 Fit side-chains REVERT: C 39 GLN cc_start: 0.7286 (tp40) cc_final: 0.6699 (tp40) REVERT: C 45 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7450 (mtt180) REVERT: A 133 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: A 214 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5963 (mp0) REVERT: A 257 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5677 (tt) REVERT: A 301 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7143 (tt) outliers start: 34 outliers final: 21 residues processed: 144 average time/residue: 0.1618 time to fit residues: 28.7961 Evaluate side-chains 151 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.0030 chunk 43 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.0642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4086 Z= 0.206 Angle : 0.639 8.658 5587 Z= 0.319 Chirality : 0.042 0.170 701 Planarity : 0.005 0.043 715 Dihedral : 5.317 48.817 576 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 8.37 % Allowed : 29.53 % Favored : 62.09 % 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: -2.78 (0.34), residues: 549 helix: -1.12 (0.57), residues: 102 sheet: -1.75 (0.44), residues: 129 loop : -2.18 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 36 HIS 0.001 0.000 HIS C 109 PHE 0.015 0.002 PHE A 410 TYR 0.006 0.001 TYR C 94 ARG 0.006 0.001 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 0.482 Fit side-chains REVERT: C 39 GLN cc_start: 0.7248 (tp40) cc_final: 0.6970 (tp40) REVERT: C 45 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7429 (mtt180) REVERT: A 54 ARG cc_start: 0.7554 (mtm110) cc_final: 0.6857 (ttp80) REVERT: A 133 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: A 214 GLU cc_start: 0.6019 (OUTLIER) cc_final: 0.5688 (mp0) REVERT: A 257 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.5582 (tt) REVERT: A 301 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7236 (tt) REVERT: A 338 GLN cc_start: 0.7750 (mp10) cc_final: 0.7427 (mp10) outliers start: 36 outliers final: 25 residues processed: 144 average time/residue: 0.1717 time to fit residues: 30.4948 Evaluate side-chains 159 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4086 Z= 0.266 Angle : 0.670 7.514 5587 Z= 0.333 Chirality : 0.043 0.170 701 Planarity : 0.005 0.042 715 Dihedral : 5.543 55.761 576 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 10.00 % Allowed : 30.00 % Favored : 60.00 % 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: -2.77 (0.35), residues: 549 helix: -1.06 (0.58), residues: 102 sheet: -1.79 (0.45), residues: 130 loop : -2.17 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 36 HIS 0.001 0.001 HIS C 109 PHE 0.014 0.002 PHE A 410 TYR 0.007 0.001 TYR C 94 ARG 0.007 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 129 time to evaluate : 0.439 Fit side-chains REVERT: C 39 GLN cc_start: 0.7244 (tp40) cc_final: 0.6967 (tp40) REVERT: C 45 ARG cc_start: 0.7760 (mtm-85) cc_final: 0.6831 (mtt180) REVERT: A 133 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: A 151 LYS cc_start: 0.8760 (mmtm) cc_final: 0.8479 (mmmt) REVERT: A 257 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5583 (tt) REVERT: A 301 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7107 (tt) REVERT: A 338 GLN cc_start: 0.7687 (mp10) cc_final: 0.7362 (mp10) outliers start: 43 outliers final: 31 residues processed: 149 average time/residue: 0.1517 time to fit residues: 27.9035 Evaluate side-chains 160 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.0000 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4086 Z= 0.202 Angle : 0.627 6.991 5587 Z= 0.312 Chirality : 0.042 0.171 701 Planarity : 0.005 0.040 715 Dihedral : 5.475 59.030 576 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 10.00 % Allowed : 29.53 % Favored : 60.47 % 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: -2.73 (0.35), residues: 549 helix: -1.11 (0.58), residues: 102 sheet: -1.71 (0.45), residues: 129 loop : -2.14 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 36 HIS 0.001 0.000 HIS C 109 PHE 0.013 0.002 PHE A 115 TYR 0.005 0.001 TYR C 37 ARG 0.005 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 129 time to evaluate : 0.453 Fit side-chains REVERT: C 39 GLN cc_start: 0.7231 (tp40) cc_final: 0.6905 (tp40) REVERT: C 45 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.6971 (mtt180) REVERT: A 54 ARG cc_start: 0.7609 (mtm110) cc_final: 0.6833 (ttp80) REVERT: A 133 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: A 257 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5830 (tt) REVERT: A 301 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7223 (tt) REVERT: A 338 GLN cc_start: 0.7658 (mp10) cc_final: 0.7320 (mp10) outliers start: 43 outliers final: 34 residues processed: 152 average time/residue: 0.1543 time to fit residues: 28.9092 Evaluate side-chains 166 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4086 Z= 0.226 Angle : 0.650 6.991 5587 Z= 0.323 Chirality : 0.043 0.171 701 Planarity : 0.005 0.041 715 Dihedral : 5.487 58.889 576 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 9.77 % Allowed : 29.53 % Favored : 60.70 % 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: -2.74 (0.35), residues: 549 helix: -1.11 (0.58), residues: 102 sheet: -1.72 (0.45), residues: 129 loop : -2.15 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 36 HIS 0.001 0.001 HIS C 109 PHE 0.012 0.002 PHE A 115 TYR 0.006 0.001 TYR C 94 ARG 0.007 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 128 time to evaluate : 0.471 Fit side-chains REVERT: C 39 GLN cc_start: 0.7234 (tp40) cc_final: 0.6879 (tp40) REVERT: C 45 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7005 (mtt180) REVERT: A 13 GLU cc_start: 0.6995 (tp30) cc_final: 0.6774 (tp30) REVERT: A 54 ARG cc_start: 0.7445 (mtm110) cc_final: 0.6805 (ttp80) REVERT: A 133 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7557 (mt-10) REVERT: A 257 LEU cc_start: 0.5808 (OUTLIER) cc_final: 0.5452 (tt) REVERT: A 301 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7219 (tt) REVERT: A 338 GLN cc_start: 0.7677 (mp10) cc_final: 0.7323 (mp10) outliers start: 42 outliers final: 36 residues processed: 150 average time/residue: 0.1579 time to fit residues: 29.2101 Evaluate side-chains 166 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.0010 chunk 43 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4086 Z= 0.216 Angle : 0.641 7.126 5587 Z= 0.318 Chirality : 0.043 0.170 701 Planarity : 0.005 0.052 715 Dihedral : 5.422 55.962 576 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 10.23 % Allowed : 29.07 % Favored : 60.70 % 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: -2.72 (0.35), residues: 549 helix: -1.09 (0.59), residues: 102 sheet: -1.71 (0.45), residues: 129 loop : -2.13 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 36 HIS 0.001 0.000 HIS C 109 PHE 0.012 0.001 PHE A 115 TYR 0.006 0.001 TYR C 37 ARG 0.008 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 0.465 Fit side-chains REVERT: C 39 GLN cc_start: 0.7239 (tp40) cc_final: 0.6869 (tp40) REVERT: C 45 ARG cc_start: 0.7748 (mtm-85) cc_final: 0.6962 (mtt180) REVERT: A 133 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: A 257 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.5572 (tt) REVERT: A 301 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7208 (tt) REVERT: A 338 GLN cc_start: 0.7679 (mp10) cc_final: 0.7320 (mp10) outliers start: 44 outliers final: 38 residues processed: 151 average time/residue: 0.1577 time to fit residues: 29.4754 Evaluate side-chains 170 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 129 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 0.0020 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4086 Z= 0.185 Angle : 0.630 7.174 5587 Z= 0.311 Chirality : 0.043 0.160 701 Planarity : 0.005 0.045 715 Dihedral : 5.232 50.731 576 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 9.53 % Allowed : 30.00 % Favored : 60.47 % 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: -2.55 (0.35), residues: 549 helix: -0.91 (0.61), residues: 96 sheet: -1.69 (0.45), residues: 129 loop : -1.98 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 36 HIS 0.000 0.000 HIS C 109 PHE 0.013 0.002 PHE A 115 TYR 0.006 0.001 TYR C 37 ARG 0.007 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 134 time to evaluate : 0.465 Fit side-chains REVERT: C 39 GLN cc_start: 0.7231 (tp40) cc_final: 0.6102 (tp40) REVERT: C 45 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7129 (mtt180) REVERT: A 54 ARG cc_start: 0.7412 (mtm110) cc_final: 0.6793 (ttp80) REVERT: A 133 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: A 144 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7331 (pp) REVERT: A 151 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8292 (mmtm) REVERT: A 257 LEU cc_start: 0.5837 (OUTLIER) cc_final: 0.5598 (tt) REVERT: A 301 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7288 (tt) REVERT: A 338 GLN cc_start: 0.7679 (mp10) cc_final: 0.7328 (mp10) outliers start: 41 outliers final: 37 residues processed: 155 average time/residue: 0.1575 time to fit residues: 30.0294 Evaluate side-chains 172 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 131 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 45 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4086 Z= 0.327 Angle : 0.719 7.560 5587 Z= 0.356 Chirality : 0.045 0.177 701 Planarity : 0.005 0.048 715 Dihedral : 5.617 52.584 576 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer: Outliers : 10.47 % Allowed : 29.77 % Favored : 59.77 % 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: -2.83 (0.35), residues: 549 helix: -1.16 (0.58), residues: 102 sheet: -1.76 (0.45), residues: 130 loop : -2.22 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 36 HIS 0.001 0.001 HIS C 109 PHE 0.011 0.002 PHE A 115 TYR 0.007 0.002 TYR C 94 ARG 0.008 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 131 time to evaluate : 0.455 Fit side-chains REVERT: C 39 GLN cc_start: 0.7297 (tp40) cc_final: 0.6187 (tp40) REVERT: C 45 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7256 (mtt180) REVERT: A 144 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7369 (pp) REVERT: A 151 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8361 (mmtm) REVERT: A 214 GLU cc_start: 0.5943 (mp0) cc_final: 0.5585 (mp0) REVERT: A 257 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5809 (tt) REVERT: A 301 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7056 (tt) REVERT: A 338 GLN cc_start: 0.7742 (mp10) cc_final: 0.7388 (mp10) outliers start: 45 outliers final: 37 residues processed: 156 average time/residue: 0.1493 time to fit residues: 29.0838 Evaluate side-chains 170 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 130 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.0070 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 0.0270 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4086 Z= 0.188 Angle : 0.645 7.099 5587 Z= 0.319 Chirality : 0.043 0.172 701 Planarity : 0.005 0.046 715 Dihedral : 5.273 47.853 576 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 7.91 % Allowed : 32.33 % Favored : 59.77 % 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: -2.72 (0.35), residues: 549 helix: -1.09 (0.59), residues: 102 sheet: -1.73 (0.45), residues: 129 loop : -2.13 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 36 HIS 0.001 0.000 HIS C 109 PHE 0.013 0.002 PHE A 115 TYR 0.006 0.001 TYR C 37 ARG 0.007 0.001 ARG A 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1098 Ramachandran restraints generated. 549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 0.473 Fit side-chains REVERT: C 39 GLN cc_start: 0.7208 (tp40) cc_final: 0.6861 (tp40) REVERT: A 133 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: A 151 LYS cc_start: 0.8627 (mmtm) cc_final: 0.8363 (mmtm) REVERT: A 214 GLU cc_start: 0.5866 (mp0) cc_final: 0.5511 (mp0) REVERT: A 257 LEU cc_start: 0.5824 (OUTLIER) cc_final: 0.5563 (tt) REVERT: A 301 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7261 (tt) REVERT: A 338 GLN cc_start: 0.7700 (mp10) cc_final: 0.7347 (mp10) outliers start: 34 outliers final: 29 residues processed: 149 average time/residue: 0.1497 time to fit residues: 27.7749 Evaluate side-chains 161 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 409 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.0570 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.134503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.111817 restraints weight = 5578.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.114525 restraints weight = 3282.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.116560 restraints weight = 2352.342| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4086 Z= 0.234 Angle : 0.680 7.765 5587 Z= 0.338 Chirality : 0.044 0.208 701 Planarity : 0.005 0.047 715 Dihedral : 5.307 45.832 576 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 7.21 % Allowed : 31.86 % Favored : 60.93 % 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: -2.83 (0.35), residues: 549 helix: -1.09 (0.59), residues: 102 sheet: -1.71 (0.43), residues: 139 loop : -2.27 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 36 HIS 0.001 0.000 HIS C 109 PHE 0.016 0.002 PHE A 434 TYR 0.006 0.001 TYR C 94 ARG 0.008 0.001 ARG A 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1351.53 seconds wall clock time: 24 minutes 27.64 seconds (1467.64 seconds total)