Starting phenix.real_space_refine on Wed Jan 17 16:52:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qic_13987/01_2024/7qic_13987.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qic_13987/01_2024/7qic_13987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qic_13987/01_2024/7qic_13987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qic_13987/01_2024/7qic_13987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qic_13987/01_2024/7qic_13987.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qic_13987/01_2024/7qic_13987.pdb" } resolution = 4.1 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= 0.001 sd= 0.036 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 28 5.16 5 C 3148 2.51 5 N 809 2.21 5 O 855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 172": "OE1" <-> "OE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 399": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 4841 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2991 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 12, 'TRANS': 388} Chain: "C" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "B" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.15, per 1000 atoms: 0.65 Number of scatterers: 4841 At special positions: 0 Unit cell: (88.536, 105.462, 76.818, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 Mg 1 11.99 O 855 8.00 N 809 7.00 C 3148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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: 1.81 Conformation dependent library (CDL) restraints added in 942.8 milliseconds 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 55.4% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 57 through 70 removed outlier: 3.519A pdb=" N THR A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 removed outlier: 3.666A pdb=" N LEU A 74 " --> pdb=" O PHE A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'A' and resid 75 through 99 removed outlier: 4.061A pdb=" N ILE A 79 " --> pdb=" O TRP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 111 through 144 removed outlier: 3.955A pdb=" N PHE A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 165 Processing helix chain 'A' and resid 169 through 179 Processing helix chain 'A' and resid 180 through 192 removed outlier: 4.103A pdb=" N THR A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 211 through 227 Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.793A pdb=" N PHE A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 277 removed outlier: 3.536A pdb=" N GLN A 251 " --> pdb=" O ASP A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.851A pdb=" N ARG A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 301 through 333 removed outlier: 3.641A pdb=" N PHE A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 3.631A pdb=" N THR A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 345 removed outlier: 4.261A pdb=" N GLU A 345 " --> pdb=" O LYS A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 345' Processing helix chain 'A' and resid 346 through 364 removed outlier: 3.570A pdb=" N LYS A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 385 removed outlier: 4.010A pdb=" N GLN A 379 " --> pdb=" O MET A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 399 removed outlier: 4.013A pdb=" N LEU A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 4.327A pdb=" N MET A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 437 Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.994A pdb=" N GLU B 111 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 108 through 112' Processing sheet with id=AA1, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.998A pdb=" N GLU C 23 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 7 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR C 68 " --> pdb=" O GLN C 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.816A pdb=" N ALA C 33 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP C 98 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.859A pdb=" N LEU B 18 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.510A pdb=" N ALA B 50 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 48 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY B 35 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA B 97 " --> pdb=" O GLY B 35 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 771 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: 1.42 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1530 1.34 - 1.46: 1163 1.46 - 1.58: 2201 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 4942 Sorted by residual: bond pdb=" CA TYR A 168 " pdb=" C TYR A 168 " ideal model delta sigma weight residual 1.523 1.537 -0.013 1.34e-02 5.57e+03 1.00e+00 bond pdb=" CA VAL A 205 " pdb=" CB VAL A 205 " ideal model delta sigma weight residual 1.526 1.540 -0.014 1.55e-02 4.16e+03 7.93e-01 bond pdb=" CA TYR A 168 " pdb=" CB TYR A 168 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 7.05e-01 bond pdb=" CA CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sigma weight residual 1.527 1.548 -0.020 2.48e-02 1.63e+03 6.73e-01 bond pdb=" N TYR A 168 " pdb=" CA TYR A 168 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.67e-01 ... (remaining 4937 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.65: 121 106.65 - 113.48: 2731 113.48 - 120.31: 1779 120.31 - 127.14: 2041 127.14 - 133.97: 49 Bond angle restraints: 6721 Sorted by residual: angle pdb=" N GLU B 89 " pdb=" CA GLU B 89 " pdb=" CB GLU B 89 " ideal model delta sigma weight residual 112.78 108.06 4.72 1.53e+00 4.27e-01 9.53e+00 angle pdb=" CA ASN C 83 " pdb=" C ASN C 83 " pdb=" O ASN C 83 " ideal model delta sigma weight residual 121.67 118.16 3.51 1.26e+00 6.30e-01 7.74e+00 angle pdb=" N ASN C 32 " pdb=" CA ASN C 32 " pdb=" C ASN C 32 " ideal model delta sigma weight residual 113.43 110.05 3.38 1.26e+00 6.30e-01 7.21e+00 angle pdb=" C THR A 130 " pdb=" N PHE A 131 " pdb=" CA PHE A 131 " ideal model delta sigma weight residual 120.72 116.25 4.47 1.67e+00 3.59e-01 7.18e+00 angle pdb=" CB MET A 89 " pdb=" CG MET A 89 " pdb=" SD MET A 89 " ideal model delta sigma weight residual 112.70 104.93 7.77 3.00e+00 1.11e-01 6.71e+00 ... (remaining 6716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 2615 15.91 - 31.82: 202 31.82 - 47.73: 61 47.73 - 63.64: 8 63.64 - 79.55: 3 Dihedral angle restraints: 2889 sinusoidal: 1068 harmonic: 1821 Sorted by residual: dihedral pdb=" CA GLN B 117 " pdb=" C GLN B 117 " pdb=" N GLY B 118 " pdb=" CA GLY B 118 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 124.62 -31.62 1 1.00e+01 1.00e-02 1.43e+01 dihedral pdb=" CA VAL C 28 " pdb=" C VAL C 28 " pdb=" N PHE C 29 " pdb=" CA PHE C 29 " ideal model delta harmonic sigma weight residual 180.00 161.49 18.51 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 476 0.036 - 0.071: 238 0.071 - 0.106: 66 0.106 - 0.142: 13 0.142 - 0.177: 2 Chirality restraints: 795 Sorted by residual: chirality pdb=" CA PHE A 131 " pdb=" N PHE A 131 " pdb=" C PHE A 131 " pdb=" CB PHE A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB THR C 90 " pdb=" CA THR C 90 " pdb=" OG1 THR C 90 " pdb=" CG2 THR C 90 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA PRO A 228 " pdb=" N PRO A 228 " pdb=" C PRO A 228 " pdb=" CB PRO A 228 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 792 not shown) Planarity restraints: 837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 13 " 0.044 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO C 14 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 309 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C GLY A 309 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY A 309 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 310 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 131 " 0.014 2.00e-02 2.50e+03 1.30e-02 2.98e+00 pdb=" CG PHE A 131 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 131 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 131 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 131 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 131 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 131 " 0.001 2.00e-02 2.50e+03 ... (remaining 834 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 694 2.76 - 3.29: 4843 3.29 - 3.83: 7905 3.83 - 4.36: 8604 4.36 - 4.90: 15115 Nonbonded interactions: 37161 Sorted by model distance: nonbonded pdb=" O TYR B 94 " pdb=" OG1 THR B 119 " model vdw 2.221 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 103 " model vdw 2.269 2.440 nonbonded pdb=" O ASN A 126 " pdb=" OG1 THR A 130 " model vdw 2.296 2.440 nonbonded pdb=" O ARG B 52 " pdb=" NH1 ARG B 72 " model vdw 2.306 2.520 nonbonded pdb=" OG1 THR A 129 " pdb=" ND2 ASN A 382 " model vdw 2.341 2.520 ... (remaining 37156 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: 0.370 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: 1.510 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.400 Find NCS groups from input model: 0.140 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 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 : 0.003 0.034 4942 Z= 0.193 Angle : 0.650 8.303 6721 Z= 0.350 Chirality : 0.043 0.177 795 Planarity : 0.005 0.067 837 Dihedral : 12.831 79.553 1717 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.20 % Allowed : 0.40 % Favored : 99.40 % 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: -0.78 (0.34), residues: 633 helix: 0.77 (0.30), residues: 305 sheet: -1.57 (0.63), residues: 73 loop : -1.78 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 160 HIS 0.001 0.000 HIS A 207 PHE 0.030 0.001 PHE A 131 TYR 0.009 0.001 TYR A 185 ARG 0.009 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 0.509 Fit side-chains REVERT: A 120 LEU cc_start: 0.7446 (tt) cc_final: 0.7147 (mm) REVERT: A 182 PHE cc_start: 0.6387 (m-10) cc_final: 0.6106 (m-10) REVERT: A 246 LYS cc_start: 0.8682 (tttm) cc_final: 0.8177 (tptt) REVERT: C 14 PRO cc_start: 0.8515 (Cg_endo) cc_final: 0.8214 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.1548 time to fit residues: 28.8089 Evaluate side-chains 119 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4942 Z= 0.230 Angle : 0.593 5.949 6721 Z= 0.314 Chirality : 0.043 0.181 795 Planarity : 0.005 0.052 837 Dihedral : 4.277 20.043 686 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.16 % Favored : 90.68 % Rotamer: Outliers : 0.40 % Allowed : 5.38 % Favored : 94.22 % 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: -0.41 (0.34), residues: 633 helix: 1.21 (0.29), residues: 314 sheet: -1.46 (0.65), residues: 73 loop : -1.87 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 229 HIS 0.001 0.001 HIS A 300 PHE 0.030 0.002 PHE A 131 TYR 0.014 0.001 TYR A 185 ARG 0.007 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 0.517 Fit side-chains REVERT: A 80 MET cc_start: 0.8698 (mmp) cc_final: 0.8349 (mmt) REVERT: A 246 LYS cc_start: 0.8706 (tttm) cc_final: 0.8238 (tptt) REVERT: A 319 CYS cc_start: 0.8066 (m) cc_final: 0.7657 (t) REVERT: C 39 GLN cc_start: 0.6878 (tp-100) cc_final: 0.6663 (tp-100) REVERT: B 37 PHE cc_start: 0.8406 (m-80) cc_final: 0.8169 (m-80) REVERT: B 47 PHE cc_start: 0.8629 (t80) cc_final: 0.8376 (t80) outliers start: 2 outliers final: 0 residues processed: 145 average time/residue: 0.1583 time to fit residues: 29.4750 Evaluate side-chains 117 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 51 optimal weight: 0.0070 chunk 56 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 0.0570 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4942 Z= 0.176 Angle : 0.571 6.700 6721 Z= 0.301 Chirality : 0.043 0.175 795 Planarity : 0.004 0.053 837 Dihedral : 4.268 19.740 686 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.53 % Favored : 91.31 % Rotamer: Outliers : 0.20 % Allowed : 2.79 % Favored : 97.01 % 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: -0.39 (0.34), residues: 633 helix: 1.26 (0.29), residues: 316 sheet: -1.45 (0.64), residues: 73 loop : -1.95 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 53 HIS 0.001 0.001 HIS A 207 PHE 0.029 0.002 PHE A 131 TYR 0.009 0.001 TYR C 93 ARG 0.005 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 80 MET cc_start: 0.8782 (mmp) cc_final: 0.8290 (mmt) REVERT: A 246 LYS cc_start: 0.8725 (tttm) cc_final: 0.8222 (tptt) REVERT: A 319 CYS cc_start: 0.8294 (m) cc_final: 0.7877 (t) REVERT: B 47 PHE cc_start: 0.8597 (t80) cc_final: 0.8352 (t80) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1495 time to fit residues: 26.7308 Evaluate side-chains 123 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.0040 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 382 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4942 Z= 0.219 Angle : 0.588 5.873 6721 Z= 0.307 Chirality : 0.043 0.178 795 Planarity : 0.004 0.055 837 Dihedral : 4.259 20.082 686 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.53 % Favored : 91.31 % Rotamer: Outliers : 0.20 % Allowed : 3.39 % Favored : 96.41 % 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: -0.35 (0.34), residues: 633 helix: 1.34 (0.29), residues: 313 sheet: -1.36 (0.64), residues: 73 loop : -1.98 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 53 HIS 0.001 0.001 HIS A 300 PHE 0.028 0.001 PHE A 131 TYR 0.013 0.001 TYR A 185 ARG 0.004 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 142 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7768 (tm-30) REVERT: A 246 LYS cc_start: 0.8758 (tttm) cc_final: 0.8202 (tptt) REVERT: A 319 CYS cc_start: 0.8312 (m) cc_final: 0.7948 (t) REVERT: C 14 PRO cc_start: 0.8759 (Cg_endo) cc_final: 0.8458 (Cg_exo) REVERT: B 47 PHE cc_start: 0.8648 (t80) cc_final: 0.8272 (t80) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.1623 time to fit residues: 29.2905 Evaluate side-chains 120 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.0070 chunk 25 optimal weight: 0.0370 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4942 Z= 0.180 Angle : 0.577 6.120 6721 Z= 0.298 Chirality : 0.043 0.169 795 Planarity : 0.004 0.055 837 Dihedral : 4.215 19.772 686 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.20 % Allowed : 2.59 % Favored : 97.21 % 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: -0.32 (0.34), residues: 633 helix: 1.38 (0.29), residues: 315 sheet: -1.45 (0.60), residues: 84 loop : -1.98 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 53 HIS 0.001 0.000 HIS A 207 PHE 0.029 0.001 PHE A 131 TYR 0.009 0.001 TYR A 185 ARG 0.006 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 0.506 Fit side-chains REVERT: A 89 MET cc_start: 0.7776 (tpt) cc_final: 0.7433 (ttt) REVERT: A 246 LYS cc_start: 0.8707 (tttm) cc_final: 0.8212 (tptt) REVERT: A 319 CYS cc_start: 0.8399 (m) cc_final: 0.8152 (t) REVERT: B 47 PHE cc_start: 0.8574 (t80) cc_final: 0.8288 (t80) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1277 time to fit residues: 22.5758 Evaluate side-chains 115 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.0020 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 0.0670 chunk 15 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 0.0570 overall best weight: 0.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 73 ASN C 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4942 Z= 0.163 Angle : 0.569 8.022 6721 Z= 0.296 Chirality : 0.042 0.175 795 Planarity : 0.005 0.070 837 Dihedral : 4.147 19.660 686 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.20 % Allowed : 1.79 % Favored : 98.01 % 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: -0.26 (0.34), residues: 633 helix: 1.38 (0.29), residues: 319 sheet: -1.40 (0.61), residues: 79 loop : -1.94 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 53 HIS 0.001 0.000 HIS A 207 PHE 0.015 0.001 PHE C 50 TYR 0.009 0.001 TYR A 185 ARG 0.006 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.511 Fit side-chains REVERT: A 252 LYS cc_start: 0.7914 (tptm) cc_final: 0.7623 (ttpt) REVERT: A 319 CYS cc_start: 0.8397 (m) cc_final: 0.8080 (t) REVERT: A 385 ILE cc_start: 0.8121 (tp) cc_final: 0.7764 (tp) REVERT: B 47 PHE cc_start: 0.8547 (t80) cc_final: 0.8317 (t80) outliers start: 1 outliers final: 1 residues processed: 134 average time/residue: 0.1285 time to fit residues: 23.2284 Evaluate side-chains 117 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.0070 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4942 Z= 0.204 Angle : 0.615 6.931 6721 Z= 0.312 Chirality : 0.043 0.176 795 Planarity : 0.005 0.058 837 Dihedral : 4.182 19.891 686 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: -0.14 (0.34), residues: 633 helix: 1.54 (0.29), residues: 312 sheet: -1.30 (0.62), residues: 79 loop : -1.90 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 53 HIS 0.001 0.001 HIS A 207 PHE 0.020 0.001 PHE C 50 TYR 0.010 0.001 TYR A 185 ARG 0.007 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.529 Fit side-chains REVERT: A 142 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7873 (tm-30) REVERT: A 319 CYS cc_start: 0.8435 (m) cc_final: 0.8227 (t) REVERT: C 58 ASN cc_start: 0.8731 (p0) cc_final: 0.8392 (p0) REVERT: B 47 PHE cc_start: 0.8601 (t80) cc_final: 0.8284 (t80) REVERT: B 83 MET cc_start: 0.6113 (mmt) cc_final: 0.5753 (mmm) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1534 time to fit residues: 27.5324 Evaluate side-chains 118 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 76 ASN B 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4942 Z= 0.234 Angle : 0.615 7.385 6721 Z= 0.316 Chirality : 0.043 0.182 795 Planarity : 0.005 0.059 837 Dihedral : 4.219 20.020 686 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.20 % Allowed : 1.99 % Favored : 97.81 % 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: -0.16 (0.34), residues: 633 helix: 1.51 (0.29), residues: 313 sheet: -1.37 (0.62), residues: 79 loop : -1.88 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 115 HIS 0.002 0.001 HIS A 207 PHE 0.020 0.001 PHE C 50 TYR 0.014 0.001 TYR A 185 ARG 0.011 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 0.506 Fit side-chains REVERT: A 89 MET cc_start: 0.7795 (tpt) cc_final: 0.7442 (ttp) REVERT: A 182 PHE cc_start: 0.6680 (m-10) cc_final: 0.6392 (m-10) REVERT: A 246 LYS cc_start: 0.8614 (tttp) cc_final: 0.8162 (tptt) REVERT: A 319 CYS cc_start: 0.8431 (m) cc_final: 0.8210 (t) REVERT: C 14 PRO cc_start: 0.8724 (Cg_exo) cc_final: 0.8449 (Cg_endo) REVERT: C 58 ASN cc_start: 0.8824 (p0) cc_final: 0.8227 (p0) REVERT: C 79 TYR cc_start: 0.8700 (m-80) cc_final: 0.8480 (m-10) REVERT: B 47 PHE cc_start: 0.8533 (t80) cc_final: 0.8256 (t80) REVERT: B 83 MET cc_start: 0.6125 (mmt) cc_final: 0.5780 (mmm) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1374 time to fit residues: 25.1701 Evaluate side-chains 121 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 53 optimal weight: 0.0470 chunk 56 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 13 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4942 Z= 0.210 Angle : 0.627 8.278 6721 Z= 0.323 Chirality : 0.044 0.180 795 Planarity : 0.005 0.060 837 Dihedral : 4.230 19.804 686 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.20 % Allowed : 0.40 % Favored : 99.40 % 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: -0.15 (0.34), residues: 633 helix: 1.53 (0.29), residues: 311 sheet: -1.38 (0.61), residues: 84 loop : -1.86 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 53 HIS 0.011 0.003 HIS B 31 PHE 0.015 0.001 PHE C 50 TYR 0.015 0.001 TYR A 185 ARG 0.012 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 0.532 Fit side-chains REVERT: A 142 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7872 (tm-30) REVERT: A 246 LYS cc_start: 0.8605 (tttp) cc_final: 0.8121 (tptt) REVERT: A 319 CYS cc_start: 0.8360 (m) cc_final: 0.8157 (t) REVERT: C 14 PRO cc_start: 0.8713 (Cg_exo) cc_final: 0.8385 (Cg_endo) REVERT: C 58 ASN cc_start: 0.8790 (p0) cc_final: 0.8181 (p0) REVERT: B 47 PHE cc_start: 0.8535 (t80) cc_final: 0.8245 (t80) REVERT: B 83 MET cc_start: 0.6144 (mmt) cc_final: 0.5794 (mmm) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1294 time to fit residues: 24.2093 Evaluate side-chains 123 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.0870 chunk 57 optimal weight: 0.0040 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 46 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 overall best weight: 0.1968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4942 Z= 0.177 Angle : 0.592 6.888 6721 Z= 0.307 Chirality : 0.043 0.190 795 Planarity : 0.005 0.061 837 Dihedral : 4.173 19.780 686 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.20 % Allowed : 0.20 % Favored : 99.60 % 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: -0.02 (0.34), residues: 633 helix: 1.68 (0.29), residues: 316 sheet: -1.40 (0.62), residues: 79 loop : -1.90 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 53 HIS 0.005 0.001 HIS B 31 PHE 0.015 0.001 PHE A 131 TYR 0.021 0.001 TYR A 185 ARG 0.009 0.000 ARG C 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 0.528 Fit side-chains REVERT: A 89 MET cc_start: 0.8090 (tpp) cc_final: 0.7815 (tpt) REVERT: A 150 LEU cc_start: 0.8472 (mm) cc_final: 0.8144 (tp) REVERT: A 182 PHE cc_start: 0.6625 (m-10) cc_final: 0.6400 (m-10) REVERT: A 319 CYS cc_start: 0.8351 (m) cc_final: 0.8067 (t) REVERT: A 385 ILE cc_start: 0.7841 (tp) cc_final: 0.7502 (tp) REVERT: C 14 PRO cc_start: 0.8738 (Cg_exo) cc_final: 0.8321 (Cg_endo) REVERT: C 58 ASN cc_start: 0.8630 (p0) cc_final: 0.8240 (p0) REVERT: B 47 PHE cc_start: 0.8470 (t80) cc_final: 0.8259 (t80) REVERT: B 83 MET cc_start: 0.6090 (mmt) cc_final: 0.5754 (mmm) outliers start: 1 outliers final: 1 residues processed: 141 average time/residue: 0.1400 time to fit residues: 26.4212 Evaluate side-chains 125 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 13 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.157063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.139406 restraints weight = 6463.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.138552 restraints weight = 6066.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.138819 restraints weight = 6024.442| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4942 Z= 0.223 Angle : 0.641 8.577 6721 Z= 0.326 Chirality : 0.044 0.183 795 Planarity : 0.005 0.061 837 Dihedral : 4.181 19.772 686 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.19 (0.34), residues: 633 helix: 1.43 (0.29), residues: 321 sheet: -1.31 (0.62), residues: 79 loop : -1.94 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 53 HIS 0.006 0.002 HIS B 31 PHE 0.017 0.001 PHE A 131 TYR 0.012 0.001 TYR A 185 ARG 0.013 0.000 ARG C 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1372.74 seconds wall clock time: 25 minutes 25.13 seconds (1525.13 seconds total)