Starting phenix.real_space_refine on Thu Dec 7 16:15:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea0_27970/12_2023/8ea0_27970.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea0_27970/12_2023/8ea0_27970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea0_27970/12_2023/8ea0_27970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea0_27970/12_2023/8ea0_27970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea0_27970/12_2023/8ea0_27970.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea0_27970/12_2023/8ea0_27970.pdb" } resolution = 2.56 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 1531 2.51 5 N 355 2.21 5 O 383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2286 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2286 Unusual residues: {'IXO': 1, 'Y01': 1} Classifications: {'peptide': 285, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 275, None: 2} Not linked: pdbres="CYS A 563 " pdbres="IXO A 801 " Not linked: pdbres="IXO A 801 " pdbres="Y01 A 802 " Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 2.00, per 1000 atoms: 0.87 Number of scatterers: 2286 At special positions: 0 Unit cell: (64.24, 74.8, 68.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 383 8.00 N 355 7.00 C 1531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 520 " 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: 1.05 Conformation dependent library (CDL) restraints added in 425.6 milliseconds 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 546 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 85.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 64 through 96 removed outlier: 3.604A pdb=" N VAL A 68 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N PHE A 70 " --> pdb=" O TRP A 66 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 104 through 120 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.864A pdb=" N THR A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 172 removed outlier: 3.560A pdb=" N CYS A 141 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 142 " --> pdb=" O ASN A 138 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.824A pdb=" N LYS A 179 " --> pdb=" O THR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 removed outlier: 4.034A pdb=" N VAL A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TRP A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Proline residue: A 202 - end of helix removed outlier: 5.186A pdb=" N GLN A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 240 Processing helix chain 'A' and resid 240 through 265 removed outlier: 3.511A pdb=" N GLU A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 503 Processing helix chain 'A' and resid 504 through 517 removed outlier: 4.035A pdb=" N LEU A 512 " --> pdb=" O ASN A 508 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 515 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 534 removed outlier: 3.541A pdb=" N CYS A 533 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 545 removed outlier: 3.570A pdb=" N THR A 538 " --> pdb=" O TYR A 534 " (cutoff:3.500A) Proline residue: A 541 - end of helix Processing helix chain 'A' and resid 548 through 561 160 hydrogen bonds defined for protein. 480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.59 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 330 1.31 - 1.43: 665 1.43 - 1.56: 1328 1.56 - 1.68: 0 1.68 - 1.81: 24 Bond restraints: 2347 Sorted by residual: bond pdb=" CAY Y01 A 802 " pdb=" OAW Y01 A 802 " ideal model delta sigma weight residual 1.332 1.376 -0.044 2.00e-02 2.50e+03 4.91e+00 bond pdb=" N11 IXO A 801 " pdb=" O12 IXO A 801 " ideal model delta sigma weight residual 1.385 1.425 -0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" C10 IXO A 801 " pdb=" N11 IXO A 801 " ideal model delta sigma weight residual 1.270 1.307 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" CBC Y01 A 802 " pdb=" OAW Y01 A 802 " ideal model delta sigma weight residual 1.437 1.417 0.020 2.00e-02 2.50e+03 9.92e-01 bond pdb=" CAX Y01 A 802 " pdb=" OAF Y01 A 802 " ideal model delta sigma weight residual 1.247 1.266 -0.019 2.00e-02 2.50e+03 8.76e-01 ... (remaining 2342 not shown) Histogram of bond angle deviations from ideal: 99.76 - 115.65: 1529 115.65 - 131.53: 1674 131.53 - 147.41: 9 147.41 - 163.29: 0 163.29 - 179.17: 2 Bond angle restraints: 3214 Sorted by residual: angle pdb=" CBB Y01 A 802 " pdb=" CBE Y01 A 802 " pdb=" CBI Y01 A 802 " ideal model delta sigma weight residual 119.27 112.25 7.02 3.00e+00 1.11e-01 5.47e+00 angle pdb=" CAJ Y01 A 802 " pdb=" CAO Y01 A 802 " pdb=" CBB Y01 A 802 " ideal model delta sigma weight residual 115.08 108.22 6.86 3.00e+00 1.11e-01 5.23e+00 angle pdb=" C PHE A 197 " pdb=" N VAL A 198 " pdb=" CA VAL A 198 " ideal model delta sigma weight residual 121.97 118.19 3.78 1.80e+00 3.09e-01 4.41e+00 angle pdb=" N LEU A 199 " pdb=" CA LEU A 199 " pdb=" C LEU A 199 " ideal model delta sigma weight residual 114.62 112.39 2.23 1.14e+00 7.69e-01 3.83e+00 angle pdb=" CAL Y01 A 802 " pdb=" CAM Y01 A 802 " pdb=" CAY Y01 A 802 " ideal model delta sigma weight residual 113.76 108.11 5.65 3.00e+00 1.11e-01 3.55e+00 ... (remaining 3209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 1391 34.98 - 69.97: 17 69.97 - 104.95: 1 104.95 - 139.93: 0 139.93 - 174.91: 1 Dihedral angle restraints: 1410 sinusoidal: 568 harmonic: 842 Sorted by residual: dihedral pdb=" CB CYS A 517 " pdb=" SG CYS A 517 " pdb=" SG CYS A 520 " pdb=" CB CYS A 520 " ideal model delta sinusoidal sigma weight residual 93.00 179.16 -86.16 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" C05 IXO A 801 " pdb=" C06 IXO A 801 " pdb=" C07 IXO A 801 " pdb=" C08 IXO A 801 " ideal model delta sinusoidal sigma weight residual 181.37 6.46 174.91 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA VAL A 198 " pdb=" C VAL A 198 " pdb=" N LEU A 199 " pdb=" CA LEU A 199 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 1407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 363 0.067 - 0.134: 24 0.134 - 0.202: 0 0.202 - 0.269: 1 0.269 - 0.336: 2 Chirality restraints: 390 Sorted by residual: chirality pdb=" CBG Y01 A 802 " pdb=" CAQ Y01 A 802 " pdb=" CBD Y01 A 802 " pdb=" CBI Y01 A 802 " both_signs ideal model delta sigma weight residual False -2.33 -2.67 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CBF Y01 A 802 " pdb=" CAS Y01 A 802 " pdb=" CBD Y01 A 802 " pdb=" CBH Y01 A 802 " both_signs ideal model delta sigma weight residual False -2.45 -2.73 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CBE Y01 A 802 " pdb=" CAP Y01 A 802 " pdb=" CBB Y01 A 802 " pdb=" CBI Y01 A 802 " both_signs ideal model delta sigma weight residual False 2.57 2.79 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 387 not shown) Planarity restraints: 375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 225 " 0.011 2.00e-02 2.50e+03 9.62e-03 1.62e+00 pdb=" CG PHE A 225 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 225 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 225 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 225 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 225 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 225 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 242 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 243 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 133 " 0.083 9.50e-02 1.11e+02 3.71e-02 8.49e-01 pdb=" NE ARG A 133 " -0.005 2.00e-02 2.50e+03 pdb=" CZ ARG A 133 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 133 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 133 " 0.003 2.00e-02 2.50e+03 ... (remaining 372 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 444 2.77 - 3.30: 2235 3.30 - 3.83: 3720 3.83 - 4.37: 4384 4.37 - 4.90: 7587 Nonbonded interactions: 18370 Sorted by model distance: nonbonded pdb=" OG1 THR A 82 " pdb=" OG1 THR A 538 " model vdw 2.237 2.440 nonbonded pdb=" O ILE A 501 " pdb=" OG1 THR A 505 " model vdw 2.282 2.440 nonbonded pdb=" O ILE A 246 " pdb=" CD1 LEU A 250 " model vdw 2.286 3.460 nonbonded pdb=" O VAL A 119 " pdb=" ND2 ASN A 123 " model vdw 2.341 2.520 nonbonded pdb=" OE1 GLN A 208 " pdb=" NE ARG A 214 " model vdw 2.346 2.520 ... (remaining 18365 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.850 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.180 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 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 0.044 2347 Z= 0.168 Angle : 0.555 7.018 3214 Z= 0.253 Chirality : 0.045 0.336 390 Planarity : 0.004 0.037 375 Dihedral : 13.659 174.912 858 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -0.24 (0.51), residues: 281 helix: 0.28 (0.35), residues: 218 sheet: None (None), residues: 0 loop : -1.38 (0.87), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 531 PHE 0.022 0.001 PHE A 225 TYR 0.006 0.001 TYR A 241 ARG 0.001 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.231 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.8689 time to fit residues: 43.8037 Evaluate side-chains 39 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.201 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.0870 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.0980 chunk 8 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 153 ASN A 536 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2347 Z= 0.191 Angle : 0.545 5.505 3214 Z= 0.289 Chirality : 0.040 0.126 390 Planarity : 0.004 0.027 375 Dihedral : 7.155 53.412 387 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.52 % Allowed : 7.14 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.53), residues: 281 helix: 1.39 (0.36), residues: 219 sheet: None (None), residues: 0 loop : -1.58 (0.89), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 252 PHE 0.030 0.002 PHE A 225 TYR 0.010 0.001 TYR A 530 ARG 0.002 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.260 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 42 average time/residue: 0.9581 time to fit residues: 41.4739 Evaluate side-chains 40 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.257 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 13 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 17 optimal weight: 0.3980 chunk 27 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2347 Z= 0.213 Angle : 0.535 5.225 3214 Z= 0.279 Chirality : 0.041 0.185 390 Planarity : 0.004 0.031 375 Dihedral : 7.131 54.208 387 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.10 % Allowed : 11.34 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.54), residues: 281 helix: 1.60 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -1.49 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.025 0.001 PHE A 225 TYR 0.015 0.001 TYR A 544 ARG 0.003 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.277 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.9584 time to fit residues: 40.5107 Evaluate side-chains 41 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.261 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.7172 time to fit residues: 2.5613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.0000 chunk 6 optimal weight: 0.8980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2347 Z= 0.213 Angle : 0.535 5.225 3214 Z= 0.279 Chirality : 0.041 0.185 390 Planarity : 0.004 0.031 375 Dihedral : 7.131 54.208 387 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.42 % Allowed : 13.87 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.54), residues: 281 helix: 1.60 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -1.49 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.025 0.001 PHE A 225 TYR 0.015 0.001 TYR A 544 ARG 0.003 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.250 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.9287 time to fit residues: 36.3438 Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.247 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 5 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.0010 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 overall best weight: 0.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2347 Z= 0.213 Angle : 0.535 5.225 3214 Z= 0.279 Chirality : 0.041 0.185 390 Planarity : 0.004 0.031 375 Dihedral : 7.131 54.208 387 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.42 % Allowed : 13.87 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.54), residues: 281 helix: 1.60 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -1.49 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.025 0.001 PHE A 225 TYR 0.015 0.001 TYR A 544 ARG 0.003 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.263 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.9382 time to fit residues: 36.7815 Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.243 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 12 optimal weight: 0.0170 chunk 10 optimal weight: 0.0980 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.0270 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2347 Z= 0.213 Angle : 0.535 5.225 3214 Z= 0.279 Chirality : 0.041 0.185 390 Planarity : 0.004 0.031 375 Dihedral : 7.131 54.208 387 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.42 % Allowed : 13.87 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.54), residues: 281 helix: 1.60 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -1.49 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.025 0.001 PHE A 225 TYR 0.015 0.001 TYR A 544 ARG 0.003 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.268 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.9274 time to fit residues: 36.3613 Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.258 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 10 optimal weight: 0.0980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2347 Z= 0.213 Angle : 0.535 5.225 3214 Z= 0.279 Chirality : 0.041 0.185 390 Planarity : 0.004 0.031 375 Dihedral : 7.131 54.208 387 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.42 % Allowed : 13.87 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.54), residues: 281 helix: 1.60 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -1.49 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.025 0.001 PHE A 225 TYR 0.015 0.001 TYR A 544 ARG 0.003 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.245 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.9574 time to fit residues: 37.4925 Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.261 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 chunk 27 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2347 Z= 0.213 Angle : 0.535 5.225 3214 Z= 0.279 Chirality : 0.041 0.185 390 Planarity : 0.004 0.031 375 Dihedral : 7.131 54.208 387 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.42 % Allowed : 13.87 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.54), residues: 281 helix: 1.60 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -1.49 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.025 0.001 PHE A 225 TYR 0.015 0.001 TYR A 544 ARG 0.003 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.192 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.9387 time to fit residues: 36.7346 Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.255 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 6 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2347 Z= 0.213 Angle : 0.535 5.225 3214 Z= 0.279 Chirality : 0.041 0.185 390 Planarity : 0.004 0.031 375 Dihedral : 7.131 54.208 387 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.42 % Allowed : 13.87 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.54), residues: 281 helix: 1.60 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -1.49 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.025 0.001 PHE A 225 TYR 0.015 0.001 TYR A 544 ARG 0.003 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.262 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.9202 time to fit residues: 36.1168 Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.268 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.0570 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.0270 chunk 19 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 10 optimal weight: 0.0980 chunk 27 optimal weight: 0.4980 chunk 1 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2347 Z= 0.213 Angle : 0.535 5.225 3214 Z= 0.279 Chirality : 0.041 0.185 390 Planarity : 0.004 0.031 375 Dihedral : 7.131 54.208 387 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.42 % Allowed : 13.87 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.54), residues: 281 helix: 1.60 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -1.49 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.025 0.001 PHE A 225 TYR 0.015 0.001 TYR A 544 ARG 0.003 0.000 ARG A 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.258 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.9376 time to fit residues: 36.7613 Evaluate side-chains 38 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.242 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 26 optimal weight: 0.0670 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.135182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.120854 restraints weight = 2985.836| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.50 r_work: 0.3564 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2347 Z= 0.213 Angle : 0.535 5.225 3214 Z= 0.279 Chirality : 0.041 0.185 390 Planarity : 0.004 0.031 375 Dihedral : 7.131 54.208 387 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.42 % Allowed : 13.87 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.54), residues: 281 helix: 1.60 (0.37), residues: 218 sheet: None (None), residues: 0 loop : -1.49 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.025 0.001 PHE A 225 TYR 0.015 0.001 TYR A 544 ARG 0.003 0.000 ARG A 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1399.07 seconds wall clock time: 25 minutes 48.08 seconds (1548.08 seconds total)