Starting phenix.real_space_refine on Sun Mar 10 14:45:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea0_27970/03_2024/8ea0_27970.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea0_27970/03_2024/8ea0_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_27970/03_2024/8ea0_27970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea0_27970/03_2024/8ea0_27970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea0_27970/03_2024/8ea0_27970.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea0_27970/03_2024/8ea0_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-dev-5265/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: 1.92, per 1000 atoms: 0.84 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: 1.01 Conformation dependent library (CDL) restraints added in 416.8 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: 0.31 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: 0.72 Time building geometry restraints manager: 1.08 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: 1.150 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: 4.840 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.840 Find NCS groups from input model: 0.060 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:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.980 ------------------------------------------------------------------------------- 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 : 0.232 Fit side-chains REVERT: A 525 PHE cc_start: 0.7945 (m-80) cc_final: 0.7540 (m-80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.8477 time to fit residues: 42.8827 Evaluate side-chains 39 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 132 ASN A 153 ASN A 536 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2347 Z= 0.195 Angle : 0.549 5.508 3214 Z= 0.291 Chirality : 0.040 0.126 390 Planarity : 0.004 0.026 375 Dihedral : 7.131 52.197 387 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.94 % Allowed : 7.14 % Favored : 89.92 % 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: 1.09 (0.53), residues: 281 helix: 1.34 (0.36), residues: 220 sheet: None (None), residues: 0 loop : -1.50 (0.91), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.029 0.002 PHE A 225 TYR 0.009 0.001 TYR A 530 ARG 0.001 0.000 ARG A 166 *********************** 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 46 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.269 Fit side-chains REVERT: A 488 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7160 (mtmm) REVERT: A 525 PHE cc_start: 0.8015 (m-80) cc_final: 0.7475 (m-80) outliers start: 7 outliers final: 2 residues processed: 42 average time/residue: 0.9102 time to fit residues: 39.4390 Evaluate side-chains 42 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 8 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 13 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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: 0.7359 moved from start: 0.1762 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= 0.221 Angle : 0.540 5.218 3214 Z= 0.284 Chirality : 0.041 0.124 390 Planarity : 0.004 0.031 375 Dihedral : 7.141 53.251 387 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.10 % Allowed : 10.92 % Favored : 86.97 % 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: 1.26 (0.54), residues: 281 helix: 1.49 (0.36), residues: 220 sheet: None (None), residues: 0 loop : -1.56 (0.89), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.026 0.002 PHE A 225 TYR 0.015 0.001 TYR A 544 ARG 0.004 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 42 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.224 Fit side-chains REVERT: A 123 ASN cc_start: 0.8371 (m-40) cc_final: 0.8143 (m-40) REVERT: A 488 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7194 (mtmm) REVERT: A 525 PHE cc_start: 0.8033 (m-80) cc_final: 0.7476 (m-80) outliers start: 5 outliers final: 2 residues processed: 39 average time/residue: 0.9455 time to fit residues: 37.9429 Evaluate side-chains 40 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 550 THR 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: 0.0770 chunk 15 optimal weight: 0.0270 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 overall best weight: 0.3396 ------------------------------------------------------------------------------- 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: 0.7359 moved from start: 0.1772 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= 0.221 Angle : 0.540 5.218 3214 Z= 0.284 Chirality : 0.041 0.124 390 Planarity : 0.004 0.031 375 Dihedral : 7.141 53.251 387 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.26 % Allowed : 13.45 % Favored : 85.29 % 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: 1.26 (0.54), residues: 281 helix: 1.49 (0.36), residues: 220 sheet: None (None), residues: 0 loop : -1.56 (0.89), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.026 0.002 PHE A 225 TYR 0.015 0.001 TYR A 544 ARG 0.004 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 40 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.257 Fit side-chains REVERT: A 123 ASN cc_start: 0.8372 (m-40) cc_final: 0.8143 (m-40) REVERT: A 488 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7193 (mtmm) outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 0.9864 time to fit residues: 38.5970 Evaluate side-chains 40 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 550 THR 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: 0.0020 chunk 6 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2347 Z= 0.213 Angle : 0.530 5.411 3214 Z= 0.280 Chirality : 0.040 0.123 390 Planarity : 0.004 0.031 375 Dihedral : 7.122 53.623 387 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.10 % Allowed : 13.03 % Favored : 84.87 % 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: 1.35 (0.54), residues: 281 helix: 1.57 (0.36), residues: 218 sheet: None (None), residues: 0 loop : -1.47 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.026 0.002 PHE A 225 TYR 0.011 0.001 TYR A 544 ARG 0.001 0.000 ARG A 214 *********************** 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 43 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.248 Fit side-chains REVERT: A 123 ASN cc_start: 0.8384 (m-40) cc_final: 0.8156 (m-40) REVERT: A 488 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7212 (mtmm) REVERT: A 525 PHE cc_start: 0.8039 (m-80) cc_final: 0.7516 (m-80) outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 0.9206 time to fit residues: 37.9635 Evaluate side-chains 43 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 550 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 0.0970 chunk 15 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 12 optimal weight: 0.4980 chunk 10 optimal weight: 0.0970 chunk 8 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 overall best weight: 0.1574 ------------------------------------------------------------------------------- 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: 0.7357 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2347 Z= 0.213 Angle : 0.530 5.411 3214 Z= 0.280 Chirality : 0.040 0.123 390 Planarity : 0.004 0.031 375 Dihedral : 7.122 53.623 387 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.10 % Allowed : 13.87 % Favored : 84.03 % 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: 1.35 (0.54), residues: 281 helix: 1.57 (0.36), residues: 218 sheet: None (None), residues: 0 loop : -1.47 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.026 0.002 PHE A 225 TYR 0.011 0.001 TYR A 544 ARG 0.001 0.000 ARG A 214 *********************** 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 43 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.259 Fit side-chains REVERT: A 123 ASN cc_start: 0.8384 (m-40) cc_final: 0.8156 (m-40) REVERT: A 488 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7212 (mtmm) REVERT: A 525 PHE cc_start: 0.8039 (m-80) cc_final: 0.7523 (m-80) outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 0.9226 time to fit residues: 38.0631 Evaluate side-chains 43 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 550 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 15 optimal weight: 0.1980 chunk 10 optimal weight: 0.0870 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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: 0.7360 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2347 Z= 0.233 Angle : 0.537 5.559 3214 Z= 0.282 Chirality : 0.041 0.124 390 Planarity : 0.004 0.032 375 Dihedral : 7.152 53.754 387 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.52 % Allowed : 13.45 % Favored : 84.03 % 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: 1.33 (0.54), residues: 281 helix: 1.56 (0.36), residues: 218 sheet: None (None), residues: 0 loop : -1.51 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.024 0.002 PHE A 225 TYR 0.011 0.001 TYR A 544 ARG 0.001 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 45 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.242 Fit side-chains REVERT: A 123 ASN cc_start: 0.8388 (m-40) cc_final: 0.8160 (m-40) REVERT: A 488 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7206 (mtmm) REVERT: A 525 PHE cc_start: 0.8032 (m-80) cc_final: 0.7501 (m-80) outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 0.9298 time to fit residues: 39.2468 Evaluate side-chains 44 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 550 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 16 optimal weight: 0.0670 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2347 Z= 0.233 Angle : 0.537 5.559 3214 Z= 0.282 Chirality : 0.041 0.124 390 Planarity : 0.004 0.032 375 Dihedral : 7.151 53.754 387 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.10 % Allowed : 13.03 % Favored : 84.87 % 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: 1.33 (0.54), residues: 281 helix: 1.56 (0.36), residues: 218 sheet: None (None), residues: 0 loop : -1.51 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.024 0.002 PHE A 225 TYR 0.011 0.001 TYR A 544 ARG 0.001 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 44 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.333 Fit side-chains REVERT: A 123 ASN cc_start: 0.8388 (m-40) cc_final: 0.8160 (m-40) REVERT: A 488 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7206 (mtmm) REVERT: A 525 PHE cc_start: 0.8032 (m-80) cc_final: 0.7501 (m-80) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.9952 time to fit residues: 42.1059 Evaluate side-chains 44 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 550 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2347 Z= 0.233 Angle : 0.537 5.559 3214 Z= 0.282 Chirality : 0.041 0.124 390 Planarity : 0.004 0.032 375 Dihedral : 7.151 53.754 387 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.10 % Allowed : 13.03 % Favored : 84.87 % 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: 1.33 (0.54), residues: 281 helix: 1.56 (0.36), residues: 218 sheet: None (None), residues: 0 loop : -1.51 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.024 0.002 PHE A 225 TYR 0.011 0.001 TYR A 544 ARG 0.001 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 44 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.266 Fit side-chains REVERT: A 123 ASN cc_start: 0.8388 (m-40) cc_final: 0.8160 (m-40) REVERT: A 488 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7206 (mtmm) REVERT: A 525 PHE cc_start: 0.8032 (m-80) cc_final: 0.7501 (m-80) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.9290 time to fit residues: 39.3383 Evaluate side-chains 44 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 550 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.0010 chunk 10 optimal weight: 0.2980 chunk 27 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 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 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2347 Z= 0.233 Angle : 0.537 5.559 3214 Z= 0.282 Chirality : 0.041 0.124 390 Planarity : 0.004 0.032 375 Dihedral : 7.151 53.754 387 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.10 % Allowed : 13.03 % Favored : 84.87 % 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: 1.33 (0.54), residues: 281 helix: 1.56 (0.36), residues: 218 sheet: None (None), residues: 0 loop : -1.51 (0.88), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 252 PHE 0.024 0.002 PHE A 225 TYR 0.011 0.001 TYR A 544 ARG 0.001 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 44 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.246 Fit side-chains REVERT: A 123 ASN cc_start: 0.8388 (m-40) cc_final: 0.8160 (m-40) REVERT: A 488 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7206 (mtmm) REVERT: A 525 PHE cc_start: 0.8032 (m-80) cc_final: 0.7501 (m-80) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.9099 time to fit residues: 38.4933 Evaluate side-chains 44 residues out of total 251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 550 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.1638 > 50: distance: 61 - 84: 16.582 distance: 66 - 91: 5.636 distance: 73 - 77: 26.957 distance: 77 - 78: 14.423 distance: 78 - 79: 9.535 distance: 78 - 81: 22.234 distance: 79 - 80: 8.204 distance: 79 - 84: 35.167 distance: 81 - 82: 21.154 distance: 81 - 83: 27.604 distance: 84 - 85: 4.069 distance: 85 - 86: 7.175 distance: 85 - 88: 6.013 distance: 86 - 87: 23.730 distance: 86 - 91: 14.527 distance: 88 - 89: 14.690 distance: 88 - 90: 19.048 distance: 91 - 92: 8.288 distance: 92 - 93: 23.632 distance: 92 - 95: 21.368 distance: 93 - 94: 15.964 distance: 93 - 99: 30.405 distance: 94 - 119: 10.104 distance: 95 - 96: 12.772 distance: 96 - 97: 38.952 distance: 96 - 98: 10.312 distance: 99 - 100: 6.978 distance: 99 - 105: 14.907 distance: 100 - 101: 13.647 distance: 100 - 103: 12.751 distance: 101 - 102: 22.765 distance: 101 - 106: 15.647 distance: 102 - 131: 23.083 distance: 103 - 104: 32.355 distance: 104 - 105: 26.660 distance: 106 - 107: 11.027 distance: 107 - 108: 25.655 distance: 107 - 110: 22.447 distance: 108 - 109: 27.488 distance: 108 - 113: 32.444 distance: 110 - 111: 27.586 distance: 110 - 112: 37.484 distance: 113 - 114: 11.540 distance: 114 - 115: 21.649 distance: 114 - 117: 24.804 distance: 115 - 116: 24.069 distance: 115 - 119: 12.836 distance: 117 - 118: 22.807 distance: 119 - 120: 5.206 distance: 120 - 121: 11.939 distance: 120 - 123: 27.448 distance: 121 - 122: 24.623 distance: 121 - 131: 3.715 distance: 123 - 124: 8.372 distance: 124 - 125: 15.803 distance: 124 - 126: 18.259 distance: 125 - 127: 17.204 distance: 126 - 128: 4.330 distance: 127 - 129: 16.471 distance: 128 - 129: 12.838 distance: 129 - 130: 4.871 distance: 131 - 132: 13.775 distance: 132 - 133: 14.278 distance: 132 - 135: 37.929 distance: 133 - 134: 31.244 distance: 133 - 136: 7.811 distance: 136 - 137: 14.037 distance: 137 - 138: 26.998 distance: 137 - 140: 26.660 distance: 138 - 139: 7.574 distance: 138 - 144: 14.183 distance: 140 - 141: 19.817 distance: 141 - 142: 22.187 distance: 141 - 143: 24.567 distance: 144 - 145: 20.470 distance: 145 - 146: 24.040 distance: 145 - 148: 24.389 distance: 146 - 150: 27.623 distance: 148 - 149: 16.612