Starting phenix.real_space_refine on Wed Jul 23 08:46:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ea0_27970/07_2025/8ea0_27970.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ea0_27970/07_2025/8ea0_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/cci-nas-00/data/ceres_data/8ea0_27970/07_2025/8ea0_27970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ea0_27970/07_2025/8ea0_27970.map" model { file = "/net/cci-nas-00/data/ceres_data/8ea0_27970/07_2025/8ea0_27970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ea0_27970/07_2025/8ea0_27970.cif" } 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. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 2286 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2237 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 275} 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 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'IXO': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.81, per 1000 atoms: 1.23 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 - 3.00 Amino acid : True - 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: 0.64 Conformation dependent library (CDL) restraints added in 275.9 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: 0.20 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: 0.57 Time building geometry restraints manager: 0.73 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: 0.00 - 1.40: 3130 1.40 - 2.81: 57 2.81 - 4.21: 16 4.21 - 5.61: 8 5.61 - 7.02: 3 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 3.040 nonbonded pdb=" O ILE A 501 " pdb=" OG1 THR A 505 " model vdw 2.282 3.040 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 3.120 nonbonded pdb=" OE1 GLN A 208 " pdb=" NE ARG A 214 " model vdw 2.346 3.120 ... (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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.820 Find NCS groups from input model: 0.020 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:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.940 ------------------------------------------------------------------------------- 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 2349 Z= 0.135 Angle : 0.555 7.018 3218 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 Details of bonding type rmsd hydrogen bonds : bond 0.26243 ( 160) hydrogen bonds : angle 8.44156 ( 480) SS BOND : bond 0.00384 ( 2) SS BOND : angle 0.48657 ( 4) covalent geometry : bond 0.00283 ( 2347) covalent geometry : angle 0.55466 ( 3214) *********************** 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 to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.221 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: 0.8884 time to fit residues: 44.8405 Evaluate side-chains 39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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: 0.6980 chunk 21 optimal weight: 0.3980 chunk 11 optimal weight: 0.0970 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 536 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.133671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.119517 restraints weight = 2981.743| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.48 r_work: 0.3542 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2349 Z= 0.207 Angle : 0.612 6.224 3218 Z= 0.324 Chirality : 0.044 0.134 390 Planarity : 0.005 0.034 375 Dihedral : 7.334 54.271 387 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.52 % Allowed : 7.56 % 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: 0.78 (0.52), residues: 281 helix: 1.11 (0.36), residues: 219 sheet: None (None), residues: 0 loop : -1.49 (0.90), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 252 PHE 0.031 0.002 PHE A 225 TYR 0.011 0.002 TYR A 530 ARG 0.002 0.000 ARG A 253 Details of bonding type rmsd hydrogen bonds : bond 0.06001 ( 160) hydrogen bonds : angle 4.99364 ( 480) SS BOND : bond 0.00890 ( 2) SS BOND : angle 0.81606 ( 4) covalent geometry : bond 0.00481 ( 2347) covalent geometry : angle 0.61170 ( 3214) *********************** 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 to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.228 Fit side-chains REVERT: A 180 ARG cc_start: 0.8344 (tmm160) cc_final: 0.8128 (ttp-170) REVERT: A 488 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7379 (mtmm) REVERT: A 525 PHE cc_start: 0.8254 (m-80) cc_final: 0.7806 (m-80) outliers start: 6 outliers final: 2 residues processed: 42 average time/residue: 0.8686 time to fit residues: 37.6644 Evaluate side-chains 41 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET 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 27 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 0.0270 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.133559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.119418 restraints weight = 2977.937| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.48 r_work: 0.3543 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2349 Z= 0.179 Angle : 0.580 5.490 3218 Z= 0.306 Chirality : 0.042 0.136 390 Planarity : 0.004 0.036 375 Dihedral : 7.290 54.926 387 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.68 % Allowed : 10.50 % Favored : 87.82 % 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: 0.99 (0.53), residues: 281 helix: 1.31 (0.36), residues: 217 sheet: None (None), residues: 0 loop : -1.55 (0.86), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 252 PHE 0.027 0.002 PHE A 225 TYR 0.015 0.002 TYR A 544 ARG 0.003 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.05617 ( 160) hydrogen bonds : angle 4.86520 ( 480) SS BOND : bond 0.00821 ( 2) SS BOND : angle 0.72523 ( 4) covalent geometry : bond 0.00408 ( 2347) covalent geometry : angle 0.57976 ( 3214) *********************** 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 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.232 Fit side-chains REVERT: A 488 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7404 (mtmm) REVERT: A 525 PHE cc_start: 0.8260 (m-80) cc_final: 0.7789 (m-80) outliers start: 4 outliers final: 0 residues processed: 38 average time/residue: 0.8828 time to fit residues: 34.7126 Evaluate side-chains 37 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 0.0370 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.2258 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.133639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.119482 restraints weight = 2941.644| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.47 r_work: 0.3540 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2349 Z= 0.179 Angle : 0.580 5.490 3218 Z= 0.306 Chirality : 0.042 0.136 390 Planarity : 0.004 0.036 375 Dihedral : 7.290 54.926 387 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.42 % Allowed : 13.03 % 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: 0.99 (0.53), residues: 281 helix: 1.31 (0.36), residues: 217 sheet: None (None), residues: 0 loop : -1.55 (0.86), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 252 PHE 0.027 0.002 PHE A 225 TYR 0.015 0.002 TYR A 544 ARG 0.003 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.05617 ( 160) hydrogen bonds : angle 4.86520 ( 480) SS BOND : bond 0.00821 ( 2) SS BOND : angle 0.72523 ( 4) covalent geometry : bond 0.00408 ( 2347) covalent geometry : angle 0.57976 ( 3214) *********************** 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 37 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.236 Fit side-chains REVERT: A 488 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7416 (mtmm) REVERT: A 525 PHE cc_start: 0.8279 (m-80) cc_final: 0.7787 (m-80) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.8797 time to fit residues: 33.6549 Evaluate side-chains 37 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 19 optimal weight: 0.3980 chunk 3 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.133413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119150 restraints weight = 3010.817| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.50 r_work: 0.3535 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2349 Z= 0.206 Angle : 0.588 5.596 3218 Z= 0.311 Chirality : 0.044 0.137 390 Planarity : 0.005 0.037 375 Dihedral : 7.307 55.127 387 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.68 % Allowed : 12.61 % 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: 0.91 (0.53), residues: 281 helix: 1.27 (0.36), residues: 218 sheet: None (None), residues: 0 loop : -1.69 (0.87), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 252 PHE 0.026 0.002 PHE A 225 TYR 0.012 0.002 TYR A 544 ARG 0.002 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.05625 ( 160) hydrogen bonds : angle 4.84408 ( 480) SS BOND : bond 0.00859 ( 2) SS BOND : angle 0.75160 ( 4) covalent geometry : bond 0.00485 ( 2347) covalent geometry : angle 0.58760 ( 3214) *********************** 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 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.270 Fit side-chains REVERT: A 180 ARG cc_start: 0.8378 (tmm160) cc_final: 0.8032 (ttp-110) REVERT: A 488 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7412 (mtmm) REVERT: A 525 PHE cc_start: 0.8285 (m-80) cc_final: 0.7822 (m-80) REVERT: A 528 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8423 (tt) outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 0.8893 time to fit residues: 34.9176 Evaluate side-chains 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 528 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.0870 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 19 optimal weight: 0.2980 chunk 27 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 11 optimal weight: 0.3980 overall best weight: 0.2158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.133363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.119222 restraints weight = 2948.935| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.47 r_work: 0.3538 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2349 Z= 0.206 Angle : 0.588 5.596 3218 Z= 0.311 Chirality : 0.043 0.137 390 Planarity : 0.005 0.037 375 Dihedral : 7.307 55.127 387 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.68 % Allowed : 12.18 % Favored : 86.13 % 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: 0.91 (0.53), residues: 281 helix: 1.27 (0.36), residues: 218 sheet: None (None), residues: 0 loop : -1.69 (0.87), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 252 PHE 0.026 0.002 PHE A 225 TYR 0.012 0.002 TYR A 544 ARG 0.002 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.05625 ( 160) hydrogen bonds : angle 4.84409 ( 480) SS BOND : bond 0.00859 ( 2) SS BOND : angle 0.75163 ( 4) covalent geometry : bond 0.00485 ( 2347) covalent geometry : angle 0.58760 ( 3214) *********************** 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 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.275 Fit side-chains REVERT: A 180 ARG cc_start: 0.8373 (tmm160) cc_final: 0.8029 (ttp-110) REVERT: A 488 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7413 (mtmm) REVERT: A 525 PHE cc_start: 0.8282 (m-80) cc_final: 0.7818 (m-80) REVERT: A 528 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8420 (tt) outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 0.8386 time to fit residues: 33.0464 Evaluate side-chains 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 528 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.0980 chunk 23 optimal weight: 0.1980 chunk 26 optimal weight: 0.3980 chunk 9 optimal weight: 0.1980 chunk 4 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 overall best weight: 0.2180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.133363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119141 restraints weight = 3001.234| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.49 r_work: 0.3536 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2349 Z= 0.206 Angle : 0.588 5.596 3218 Z= 0.311 Chirality : 0.043 0.137 390 Planarity : 0.005 0.037 375 Dihedral : 7.307 55.127 387 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.68 % Allowed : 12.18 % Favored : 86.13 % 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: 0.91 (0.53), residues: 281 helix: 1.27 (0.36), residues: 218 sheet: None (None), residues: 0 loop : -1.69 (0.87), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 252 PHE 0.026 0.002 PHE A 225 TYR 0.012 0.002 TYR A 544 ARG 0.002 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.05625 ( 160) hydrogen bonds : angle 4.84409 ( 480) SS BOND : bond 0.00859 ( 2) SS BOND : angle 0.75163 ( 4) covalent geometry : bond 0.00485 ( 2347) covalent geometry : angle 0.58760 ( 3214) *********************** 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 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.247 Fit side-chains REVERT: A 180 ARG cc_start: 0.8374 (tmm160) cc_final: 0.8031 (ttp-110) REVERT: A 488 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7415 (mtmm) REVERT: A 525 PHE cc_start: 0.8284 (m-80) cc_final: 0.7820 (m-80) REVERT: A 528 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8416 (tt) outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 0.8135 time to fit residues: 32.0291 Evaluate side-chains 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 528 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.0070 chunk 6 optimal weight: 0.0980 chunk 11 optimal weight: 0.3980 chunk 25 optimal weight: 0.3980 chunk 26 optimal weight: 0.0370 chunk 21 optimal weight: 0.5980 overall best weight: 0.1876 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.133363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.119067 restraints weight = 3048.340| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.51 r_work: 0.3534 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2349 Z= 0.206 Angle : 0.588 5.596 3218 Z= 0.311 Chirality : 0.043 0.137 390 Planarity : 0.005 0.037 375 Dihedral : 7.307 55.127 387 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.68 % Allowed : 12.18 % Favored : 86.13 % 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: 0.91 (0.53), residues: 281 helix: 1.27 (0.36), residues: 218 sheet: None (None), residues: 0 loop : -1.69 (0.87), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 252 PHE 0.026 0.002 PHE A 225 TYR 0.012 0.002 TYR A 544 ARG 0.002 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.05625 ( 160) hydrogen bonds : angle 4.84409 ( 480) SS BOND : bond 0.00859 ( 2) SS BOND : angle 0.75163 ( 4) covalent geometry : bond 0.00485 ( 2347) covalent geometry : angle 0.58760 ( 3214) *********************** 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 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.258 Fit side-chains REVERT: A 180 ARG cc_start: 0.8374 (tmm160) cc_final: 0.8031 (ttp-110) REVERT: A 488 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7414 (mtmm) REVERT: A 525 PHE cc_start: 0.8286 (m-80) cc_final: 0.7823 (m-80) REVERT: A 528 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8417 (tt) outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 0.8510 time to fit residues: 33.4112 Evaluate side-chains 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 528 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 19 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 18 optimal weight: 0.3980 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.133363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119121 restraints weight = 3003.828| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.49 r_work: 0.3535 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2349 Z= 0.206 Angle : 0.588 5.596 3218 Z= 0.311 Chirality : 0.043 0.137 390 Planarity : 0.005 0.037 375 Dihedral : 7.307 55.127 387 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.68 % Allowed : 12.18 % Favored : 86.13 % 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: 0.91 (0.53), residues: 281 helix: 1.27 (0.36), residues: 218 sheet: None (None), residues: 0 loop : -1.69 (0.87), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 252 PHE 0.026 0.002 PHE A 225 TYR 0.012 0.002 TYR A 544 ARG 0.002 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.05625 ( 160) hydrogen bonds : angle 4.84409 ( 480) SS BOND : bond 0.00859 ( 2) SS BOND : angle 0.75163 ( 4) covalent geometry : bond 0.00485 ( 2347) covalent geometry : angle 0.58760 ( 3214) *********************** 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 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.224 Fit side-chains REVERT: A 180 ARG cc_start: 0.8374 (tmm160) cc_final: 0.8031 (ttp-110) REVERT: A 488 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7414 (mtmm) REVERT: A 525 PHE cc_start: 0.8287 (m-80) cc_final: 0.7824 (m-80) REVERT: A 528 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8421 (tt) outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 0.8863 time to fit residues: 34.7939 Evaluate side-chains 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 528 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 0.0970 chunk 25 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.133363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.119191 restraints weight = 2966.822| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.48 r_work: 0.3537 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2349 Z= 0.206 Angle : 0.588 5.596 3218 Z= 0.311 Chirality : 0.043 0.137 390 Planarity : 0.005 0.037 375 Dihedral : 7.307 55.127 387 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.68 % Allowed : 12.18 % Favored : 86.13 % 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: 0.91 (0.53), residues: 281 helix: 1.27 (0.36), residues: 218 sheet: None (None), residues: 0 loop : -1.69 (0.87), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 252 PHE 0.026 0.002 PHE A 225 TYR 0.012 0.002 TYR A 544 ARG 0.002 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.05625 ( 160) hydrogen bonds : angle 4.84409 ( 480) SS BOND : bond 0.00859 ( 2) SS BOND : angle 0.75163 ( 4) covalent geometry : bond 0.00485 ( 2347) covalent geometry : angle 0.58760 ( 3214) ********************** 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 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.224 Fit side-chains REVERT: A 180 ARG cc_start: 0.8373 (tmm160) cc_final: 0.8030 (ttp-110) REVERT: A 488 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7414 (mtmm) REVERT: A 525 PHE cc_start: 0.8282 (m-80) cc_final: 0.7818 (m-80) REVERT: A 528 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8416 (tt) outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 0.8349 time to fit residues: 32.7937 Evaluate side-chains 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 528 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.133363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119176 restraints weight = 2975.532| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.48 r_work: 0.3536 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2349 Z= 0.206 Angle : 0.588 5.596 3218 Z= 0.311 Chirality : 0.043 0.137 390 Planarity : 0.005 0.037 375 Dihedral : 7.307 55.127 387 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.68 % Allowed : 12.18 % Favored : 86.13 % 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: 0.91 (0.53), residues: 281 helix: 1.27 (0.36), residues: 218 sheet: None (None), residues: 0 loop : -1.69 (0.87), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 252 PHE 0.026 0.002 PHE A 225 TYR 0.012 0.002 TYR A 544 ARG 0.002 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.05625 ( 160) hydrogen bonds : angle 4.84409 ( 480) SS BOND : bond 0.00859 ( 2) SS BOND : angle 0.75163 ( 4) covalent geometry : bond 0.00485 ( 2347) covalent geometry : angle 0.58760 ( 3214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2262.63 seconds wall clock time: 39 minutes 30.65 seconds (2370.65 seconds total)